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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 files COPYING and Copyright.html. COPYING can be found at the root *
+ * of the source code distribution tree; Copyright.html can be found at the *
+ * root level of an installed copy of the electronic HDF5 document set and *
+ * is linked from the top-level documents page. It can also be found at *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
+ * access to either file, you may request a copy from help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/****************/
+/* Module Setup */
+/****************/
+
+#define H5D_PACKAGE /*suppress error about including H5Dpkg */
+
+/* Interface initialization */
+#define H5_INTERFACE_INIT_FUNC H5D_init_interface
+
+
+/***********/
+/* Headers */
+/***********/
+#include "H5private.h" /* Generic Functions */
+#include "H5Dpkg.h" /* Datasets */
+#include "H5Eprivate.h" /* Error handling */
+#include "H5FOprivate.h" /* File objects */
+#include "H5HLprivate.h" /* Local heaps */
+#include "H5Iprivate.h" /* IDs */
+#include "H5Lprivate.h" /* Links */
+#include "H5MMprivate.h" /* Memory management */
+
+
+/****************/
+/* Local Macros */
+/****************/
+
+
+/******************/
+/* Local Typedefs */
+/******************/
+
+
+/********************/
+/* Local Prototypes */
+/********************/
+
+/* General stuff */
+static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite, hid_t dxpl_id);
+static H5D_shared_t *H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type);
+static herr_t H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id,
+ const H5T_t *type);
+static herr_t H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space);
+static herr_t H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset);
+static herr_t H5D_open_oid(H5D_t *dataset, hid_t dxpl_id);
+
+
+/*********************/
+/* Package Variables */
+/*********************/
+
+/* Define a "default" dataset transfer property list cache structure to use for default DXPLs */
+H5D_dxpl_cache_t H5D_def_dxpl_cache;
+
+/* Declare a free list to manage blocks of VL data */
+H5FL_BLK_DEFINE(vlen_vl_buf);
+
+/* Declare a free list to manage other blocks of VL data */
+H5FL_BLK_DEFINE(vlen_fl_buf);
+
+
+/*****************************/
+/* Library Private Variables */
+/*****************************/
+
+
+/*******************/
+/* Local Variables */
+/*******************/
+
+/* Declare a free list to manage the H5D_t and H5D_shared_t structs */
+H5FL_DEFINE_STATIC(H5D_t);
+H5FL_DEFINE_STATIC(H5D_shared_t);
+
+/* Declare the external PQ free list for the sieve buffer information */
+H5FL_BLK_EXTERN(sieve_buf);
+
+/* Define a static "default" dataset structure to use to initialize new datasets */
+static H5D_shared_t H5D_def_dset;
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_init
+ *
+ * Purpose: Initialize the interface from some other layer.
+ *
+ * Return: Success: non-negative
+ *
+ * Failure: negative
+ *
+ * Programmer: Quincey Koziol
+ * Saturday, March 4, 2000
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_init(void)
+{
+ herr_t ret_value=SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_init, FAIL)
+ /* FUNC_ENTER() does all the work */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_init() */
+
+
+/*--------------------------------------------------------------------------
+NAME
+ H5D_init_interface -- Initialize interface-specific information
+USAGE
+ herr_t H5D_init_interface()
+
+RETURNS
+ Non-negative on success/Negative on failure
+DESCRIPTION
+ Initializes any interface-specific data or routines.
+NOTES
+ Care must be taken when using the H5P functions, since they can cause
+ a deadlock in the library when the library is attempting to terminate -QAK
+
+--------------------------------------------------------------------------*/
+static herr_t
+H5D_init_interface(void)
+{
+ H5P_genplist_t *def_dcpl; /* Default Dataset Creation Property list */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_init_interface)
+
+ /* Initialize the atom group for the dataset IDs */
+ if(H5I_register_type(H5I_DATASET, (size_t)H5I_DATASETID_HASHSIZE, H5D_RESERVED_ATOMS, (H5I_free_t)H5D_close)<H5I_FILE)
+ 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_g)))
+ HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get default dataset creation property list")
+
+ /* Get the default data storage method */
+ if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout.type) < 0)
+ 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, H5D_CRT_DATA_PIPELINE_NAME, &H5D_def_dset.dcpl_cache.pline) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve pipeline filter")
+
+ /* Reset the "default DXPL cache" information */
+ HDmemset(&H5D_def_dxpl_cache, 0, sizeof(H5D_dxpl_cache_t));
+
+ /* Get the default DXPL cache information */
+ if(H5D_get_dxpl_cache_real(H5P_DATASET_XFER_DEFAULT, &H5D_def_dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve default DXPL info")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_init_interface() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_term_interface
+ *
+ * Purpose: Terminate this interface.
+ *
+ * Return: Success: Positive if anything was done that might
+ * affect other interfaces; zero otherwise.
+ *
+ * Failure: Negative.
+ *
+ * Programmer: Robb Matzke
+ * Friday, November 20, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+H5D_term_interface(void)
+{
+ int n=0;
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_term_interface)
+
+ if(H5_interface_initialize_g) {
+ if((n=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
+ */
+ H5I_clear_type(H5I_DATASET, TRUE);
+ } else {
+ H5I_dec_type_ref(H5I_DATASET);
+ H5_interface_initialize_g = 0;
+ n = 1; /*H5I*/
+ }
+ }
+ FUNC_LEAVE_NOAPI(n)
+} /* end H5D_term_interface() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_create_named
+ *
+ * Purpose: Internal routine to create a new dataset.
+ *
+ * Return: Success: Non-NULL, pointer to new dataset object.
+ *
+ * Failure: NULL
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, April 5, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+H5D_t *
+H5D_create_named(const H5G_loc_t *loc, const char *name, hid_t type_id,
+ const H5S_t *space, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id,
+ hid_t dxpl_id)
+{
+ H5O_obj_create_t ocrt_info; /* Information for object creation */
+ H5D_obj_create_t dcrt_info; /* Information for dataset creation */
+ H5D_t *ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_create_named, NULL)
+
+ /* Check arguments */
+ HDassert(loc);
+ HDassert(name && *name);
+ HDassert(type_id != H5P_DEFAULT);
+ HDassert(space);
+ HDassert(lcpl_id != H5P_DEFAULT);
+ HDassert(dcpl_id != H5P_DEFAULT);
+ HDassert(dapl_id != H5P_DEFAULT);
+ HDassert(dxpl_id != H5P_DEFAULT);
+
+ /* Set up dataset creation info */
+ dcrt_info.type_id = type_id;
+ dcrt_info.space = space;
+ dcrt_info.dcpl_id = dcpl_id;
+
+ /* Set up object creation information */
+ ocrt_info.obj_type = H5O_TYPE_DATASET;
+ ocrt_info.crt_info = &dcrt_info;
+ ocrt_info.new_obj = NULL;
+
+ /* Create the new dataset and link it to its parent group */
+ if(H5L_link_object(loc, name, &ocrt_info, lcpl_id, dapl_id, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to create and link to dataset")
+ HDassert(ocrt_info.new_obj);
+
+ /* Set the return value */
+ ret_value = (H5D_t *)ocrt_info.new_obj;
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_create_named() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_get_space_status
+ *
+ * Purpose: Returns the status of data space allocation.
+ *
+ * Return:
+ * Success: Non-negative
+ *
+ * Failture: Negative
+ *
+ * Programmer: Raymond Lu
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id)
+{
+ H5S_t *space; /* Dataset's dataspace */
+ hsize_t space_allocated; /* The number of bytes allocated for chunks */
+ hssize_t total_elem; /* The total number of elements in dataspace */
+ size_t type_size; /* The size of the datatype for the dataset */
+ hsize_t full_size; /* The number of bytes in the dataset when fully populated */
+ herr_t ret_value = SUCCEED;
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_get_space_status)
+
+ HDassert(dset);
+
+ /* Get the dataset's dataspace */
+ space = dset->shared->space;
+ HDassert(space);
+
+ /* Get the total number of elements in dataset's dataspace */
+ if((total_elem=H5S_GET_EXTENT_NPOINTS(space)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get # of dataspace elements")
+
+ /* Get the size of the dataset's datatype */
+ if((type_size = H5T_get_size(dset->shared->type)) == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get size of datatype")
+
+ /* Compute the maximum size of the dataset in bytes */
+ H5_CHECK_OVERFLOW(total_elem,hssize_t,hsize_t);
+ full_size=((hsize_t)total_elem)*type_size;
+
+ /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */
+ space_allocated = H5D_get_storage_size(dset, dxpl_id);
+
+ /* Decide on how much of the space is allocated */
+ if(space_allocated == 0)
+ *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED;
+ else if(space_allocated == full_size)
+ *allocation = H5D_SPACE_STATUS_ALLOCATED;
+ else {
+ /* Should only happen for chunked datasets currently */
+ HDassert(dset->shared->layout.type == H5D_CHUNKED);
+
+ *allocation = H5D_SPACE_STATUS_PART_ALLOCATED;
+ } /* end else */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_get_space_status() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_new
+ *
+ * Purpose: Creates a new, empty dataset structure
+ *
+ * Return: Success: Pointer to a new dataset descriptor.
+ *
+ * Failure: NULL
+ *
+ * Programmer: Quincey Koziol
+ * Monday, October 12, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+static H5D_shared_t *
+H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type)
+{
+ H5P_genplist_t *plist; /* Property list created */
+ H5D_shared_t *new_dset = NULL; /* New dataset object */
+ H5D_shared_t *ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_new)
+
+ /* Allocate new shared dataset structure */
+ if(NULL == (new_dset = H5FL_MALLOC(H5D_shared_t)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
+
+ /* Copy the default dataset information */
+ HDmemcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t));
+
+ /* If we are using the default dataset creation property list, during creation
+ * don't bother to copy it, just increment the reference count
+ */
+ if(!vl_type && creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) {
+ if(H5I_inc_ref(dcpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "Can't increment default DCPL ID")
+ new_dset->dcpl_id = dcpl_id;
+ } /* end if */
+ else {
+ /* Get the property list */
+ if(NULL == (plist = (H5P_genplist_t *)H5I_object(dcpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list")
+
+ new_dset->dcpl_id = H5P_copy_plist(plist);
+ } /* end else */
+
+ /* Set return value */
+ ret_value = new_dset;
+
+done:
+ if(ret_value == NULL)
+ if(new_dset != NULL) {
+ if(new_dset->dcpl_id != 0)
+ (void)H5I_dec_ref(new_dset->dcpl_id);
+ H5FL_FREE(H5D_shared_t, new_dset);
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_new() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_init_type
+ *
+ * Purpose: Copy a datatype for a dataset's use, performing all the
+ * necessary adjustments, etc.
+ *
+ * Return: Success: SUCCEED
+ * Failure: FAIL
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, June 24, 2004
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, const H5T_t *type)
+{
+ htri_t relocatable; /* Flag whether the type is relocatable */
+ htri_t immutable; /* Flag whether the type is immutable */
+ hbool_t use_latest_format; /* Flag indicating the newest file format should be used */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_init_type)
+
+ /* Sanity checking */
+ HDassert(file);
+ HDassert(dset);
+ HDassert(type);
+
+ /* Check whether the datatype is relocatable */
+ if((relocatable = H5T_is_relocatable(type)) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?")
+
+ /* Check whether the datatype is immutable */
+ if((immutable = H5T_is_immutable(type)) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?")
+
+ /* Get the file's 'use the latest version of the format' flag */
+ use_latest_format = H5F_USE_LATEST_FORMAT(file);
+
+ /* Copy the datatype if it's a custom datatype or if it'll change when it's location is changed */
+ if(!immutable || relocatable || use_latest_format) {
+ /* Copy datatype for dataset */
+ if((dset->shared->type = H5T_copy(type, H5T_COPY_ALL)) == NULL)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy datatype")
+
+ /* Mark any datatypes as being on disk now */
+ if(H5T_set_loc(dset->shared->type, file, H5T_LOC_DISK) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't set datatype location")
+
+ /* Set the latest format, if requested */
+ if(use_latest_format)
+ if(H5T_set_latest_version(dset->shared->type) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype")
+
+ /* Get a datatype ID for the dataset's datatype */
+ if((dset->shared->type_id = H5I_register(H5I_DATATYPE, dset->shared->type)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type")
+ } /* end if */
+ /* Not a custom datatype, just use it directly */
+ else {
+ if(H5I_inc_ref(type_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment datatype ID")
+
+ /* Use existing datatype */
+ dset->shared->type_id = type_id;
+ dset->shared->type = (H5T_t *)type; /* (Cast away const OK - QAK) */
+ } /* end else */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_init_type() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_init_space
+ *
+ * Purpose: Copy a dataspace for a dataset's use, performing all the
+ * necessary adjustments, etc.
+ *
+ * Return: Success: SUCCEED
+ * Failure: FAIL
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, July 24, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space)
+{
+ hbool_t use_latest_format; /* Flag indicating the newest file format should be used */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_init_space)
+
+ /* Sanity checking */
+ HDassert(file);
+ HDassert(dset);
+ HDassert(space);
+
+ /* Get the file's 'use the latest version of the format' flag */
+ use_latest_format = H5F_USE_LATEST_FORMAT(file);
+
+ /* Copy dataspace for dataset */
+ if(NULL == (dset->shared->space = H5S_copy(space, FALSE)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dataspace")
+
+ /* Set the latest format, if requested */
+ if(use_latest_format)
+ if(H5S_set_latest_version(dset->shared->space) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype")
+
+ /* Set the dataset's dataspace to 'all' selection */
+ if(H5S_select_all(dset->shared->space, TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set all selection")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_init_space() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_update_oh_info
+ *
+ * Purpose: Create and fill object header for dataset
+ *
+ * Return: Success: SUCCEED
+ * Failure: FAIL
+ *
+ * Programmer: Bill Wendling
+ * Thursday, October 31, 2002
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset)
+{
+ struct H5O_t *oh = NULL; /* Pointer to dataset's object header */
+ size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */
+ H5O_loc_t *oloc = NULL; /* Dataset's object location */
+ H5O_layout_t *layout; /* Dataset's layout information */
+ H5T_t *type; /* Dataset's datatype */
+ hbool_t use_latest_format; /* Flag indicating the newest file format should be used */
+ H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */
+ H5D_fill_value_t fill_status; /* Fill value status */
+ hbool_t fill_changed = FALSE; /* Flag indicating the fill value was changed */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_update_oh_info)
+
+ /* Sanity checking */
+ HDassert(file);
+ HDassert(dset);
+
+ /* Set some local variables, for convenience */
+ oloc = &dset->oloc;
+ layout = &dset->shared->layout;
+ type = dset->shared->type;
+ fill_prop = &dset->shared->dcpl_cache.fill;
+
+ /* Get the file's 'use the latest version of the format' flag */
+ use_latest_format = H5F_USE_LATEST_FORMAT(file);
+
+ /* Retrieve "defined" status of fill value */
+ if(H5P_is_fill_value_defined(fill_prop, &fill_status) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
+
+ /* Special case handling for variable-length types */
+ if(H5T_detect_class(type, H5T_VLEN)) {
+ /* If the default fill value is chosen for variable-length types, always write it */
+ if(fill_prop->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_DEFAULT) {
+ /* Update dataset creation property */
+ fill_prop->fill_time = H5D_FILL_TIME_ALLOC;
+
+ /* Note that the fill value changed */
+ fill_changed = TRUE;
+ } /* end if */
+
+ /* Don't allow never writing fill values with variable-length types */
+ if(fill_prop->fill_time == H5D_FILL_TIME_NEVER)
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Dataset doesn't support VL datatype when fill value is not defined")
+ } /* end if */
+
+ /* Determine whether fill value is defined or not */
+ if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) {
+ /* Convert fill value buffer to dataset's datatype */
+ if(fill_prop->buf && fill_prop->size > 0 && H5O_fill_convert(fill_prop, type, &fill_changed, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert fill value to dataset type")
+
+ fill_prop->fill_defined = TRUE;
+ } else if(fill_status == H5D_FILL_VALUE_UNDEFINED) {
+ fill_prop->fill_defined = FALSE;
+ } else
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine if fill value is defined")
+
+ /* Check for invalid fill & allocation time setting */
+ if(fill_prop->fill_defined == FALSE && fill_prop->fill_time == H5D_FILL_TIME_ALLOC)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "fill value writing on allocation set, but no fill value defined")
+
+ /* Check if the fill value info changed */
+ if(fill_changed) {
+ H5P_genplist_t *dc_plist; /* Dataset's creation property list */
+
+ /* Get dataset's property list object */
+ HDassert(dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT);
+ if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list")
+
+ /* Update dataset creation property */
+ if(H5P_set(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value info")
+ } /* end if */
+
+ /* Add the dataset's raw data size to the size of the header, if the raw data will be stored as compact */
+ if(layout->type == H5D_COMPACT)
+ ohdr_size += layout->u.compact.size;
+
+ /* Create an object header for the dataset */
+ if(H5O_create(file, dxpl_id, ohdr_size, dset->shared->dcpl_id, oloc/*out*/) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header")
+
+ /* Get a pointer to the object header itself */
+ if((oh = H5O_protect(oloc, dxpl_id)) == NULL)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to protect dataset object header")
+
+ /* Write new fill value message */
+ if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update new fill value header message")
+
+ /* If there is valid information for the old fill value struct, add it */
+ /* (only if we aren't trying to write the latest version of the file format) */
+ if(fill_prop->buf && !use_latest_format) {
+ H5O_fill_t old_fill_prop; /* Copy of fill value property, for writing as "old" fill value */
+
+ /* Shallow copy the fill value property */
+ /* (we only want to make certain that the shared component isnt' modified) */
+ HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
+
+ /* Reset shared component info */
+ H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop);
+
+ /* Write old fill value */
+ if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_ID, H5O_MSG_FLAG_CONSTANT, 0, &old_fill_prop) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update old fill value header message")
+ } /* end if */
+
+ /* Update the datatype and dataspace header messages */
+ if(H5O_msg_append(file, dxpl_id, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update datatype header message")
+ if(H5S_append(file, dxpl_id, oh, dset->shared->space) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message")
+
+ /* Update the filters message, if this is a chunked dataset */
+ if(layout->type == H5D_CHUNKED) {
+ H5O_pline_t *pline; /* Dataset's I/O pipeline information */
+
+ pline = &dset->shared->dcpl_cache.pline;
+ if(pline->nused > 0 && H5O_msg_append(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message")
+ } /* end if */
+
+ /*
+ * Allocate storage if space allocate time is early; otherwise delay
+ * allocation until later.
+ */
+ if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY)
+ if(H5D_alloc_storage(file, dxpl_id, dset, H5D_ALLOC_CREATE, FALSE, FALSE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
+
+ /* Update external storage message, if it's used */
+ if(dset->shared->dcpl_cache.efl.nused > 0) {
+ H5O_efl_t *efl = &dset->shared->dcpl_cache.efl; /* Dataset's external file list */
+ H5HL_t *heap; /* Pointer to local heap for EFL file names */
+ size_t heap_size = H5HL_ALIGN(1);
+ size_t u;
+
+ /* Determine size of heap needed to stored the file names */
+ for(u = 0; u < efl->nused; ++u)
+ heap_size += H5HL_ALIGN(HDstrlen(efl->slot[u].name) + 1);
+
+ /* Create the heap for the EFL file names */
+ if(H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr/*out*/) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create EFL file name heap")
+
+ /* Pin the heap down in memory */
+ if(NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC_WRITE)))
+ HGOTO_ERROR(H5E_DATASET, H5E_PROTECT, FAIL, "unable to protect EFL file name heap")
+
+ /* Insert "empty" name first */
+ if((size_t)(-1) == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) {
+ H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr);
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
+ } /* end if */
+
+ for(u = 0; u < efl->nused; ++u) {
+ size_t offset; /* Offset of file name in heap */
+
+ /* Insert file name into heap */
+ if((size_t)(-1) == (offset = H5HL_insert(file, dxpl_id, heap,
+ HDstrlen(efl->slot[u].name) + 1, efl->slot[u].name))) {
+ H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr);
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
+ } /* end if */
+
+ /* Store EFL file name offset */
+ HDassert(0 == efl->slot[u].name_offset);
+ efl->slot[u].name_offset = offset;
+ } /* end for */
+
+ /* Release the heap */
+ if(H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_PROTECT, FAIL, "unable to unprotect EFL file name heap")
+ heap = NULL;
+
+ /* Insert EFL message into dataset object header */
+ if(H5O_msg_append(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message")
+ } /* end if */
+
+ /* Create layout message */
+ /* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */
+ /* (Note: this is relying on H5D_alloc_storage not calling H5O_msg_write during dataset creation) */
+ if(H5O_msg_append(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout")
+
+#ifdef H5O_ENABLE_BOGUS
+{
+ H5P_genplist_t *dc_plist; /* Dataset's creation property list */
+
+ /* Get dataset's property list object */
+ if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list")
+
+ /* Check whether to add a "bogus" message */
+ if(H5P_exist_plist(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME) > 0) {
+ uint8_t bogus_flags = 0; /* Flags for creating "bogus" message */
+
+ /* Retrieve "bogus" message flags */
+ if(H5P_get(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME, &bogus_flags) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get bogus message options")
+
+ /* Add a "bogus" message (for error testing). */
+ if(H5O_bogus_oh(file, dxpl_id, oh, (unsigned)bogus_flags) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create 'bogus' message")
+ } /* end if */
+}
+#endif /* H5O_ENABLE_BOGUS */
+
+ /* Add a modification time message. */
+ if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message")
+
+done:
+ /* Release pointer to object header itself */
+ if(oloc != NULL && oh != NULL)
+ if(H5O_unprotect(oloc, oh) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to unprotect dataset object header")
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_update_oh_info() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_create
+ *
+ * Purpose: Creates a new dataset with name NAME in file F and associates
+ * with it a datatype TYPE for each element as stored in the
+ * file, dimensionality information or dataspace SPACE, and
+ * other miscellaneous properties CREATE_PARMS. All arguments
+ * are deep-copied before being associated with the new dataset,
+ * so the caller is free to subsequently modify them without
+ * affecting the dataset.
+ *
+ * Return: Success: Pointer to a new dataset
+ *
+ * Failure: NULL
+ *
+ * Programmer: Robb Matzke
+ * Thursday, December 4, 1997
+ *
+ *-------------------------------------------------------------------------
+ */
+H5D_t *
+H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
+ hid_t dxpl_id)
+{
+ const H5T_t *type; /* Datatype for dataset */
+ H5D_t *new_dset = NULL;
+ int i, ndims;
+ unsigned chunk_ndims = 0; /* Dimensionality of chunk */
+ H5P_genplist_t *dc_plist = NULL; /* New Property list */
+ hbool_t has_vl_type = FALSE; /* Flag to indicate a VL-type for dataset */
+ hbool_t chunk_init = FALSE; /* Flag to indicate that chunk information was initialized */
+ H5G_loc_t dset_loc; /* Dataset location */
+ unsigned u; /* Local index variable */
+ H5D_t *ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_create, NULL)
+
+ /* check args */
+ HDassert(file);
+ HDassert(H5I_DATATYPE==H5I_get_type(type_id));
+ HDassert(space);
+ HDassert(H5I_GENPROP_LST==H5I_get_type(dcpl_id));
+ HDassert(H5I_GENPROP_LST==H5I_get_type(dxpl_id));
+
+ /* Get the dataset's datatype */
+ if(NULL == (type = (const H5T_t *)H5I_object(type_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a datatype")
+
+ /* Check if the datatype is "sensible" for use in a dataset */
+ if(H5T_is_sensible(type) != TRUE)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "datatype is not sensible")
+
+ /* Check if the datatype is/contains a VL-type */
+ if(H5T_detect_class(type, H5T_VLEN))
+ has_vl_type=TRUE;
+
+ /* Check if the dataspace has an extent set (or is NULL) */
+ if(!(H5S_has_extent(space)) )
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "dataspace extent has not been set.")
+
+ /* Initialize the dataset object */
+ if(NULL == (new_dset = H5FL_CALLOC(H5D_t)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
+
+ /* Set up & reset dataset location */
+ dset_loc.oloc = &(new_dset->oloc);
+ dset_loc.path = &(new_dset->path);
+ H5G_loc_reset(&dset_loc);
+
+ /* Initialize the shared dataset space */
+ if(NULL == (new_dset->shared = H5D_new(dcpl_id, TRUE, has_vl_type)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
+
+ /* Copy & initialize datatype for dataset */
+ if(H5D_init_type(file, new_dset, type_id, type) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy datatype")
+
+ /* Copy & initialize dataspace for dataset */
+ if(H5D_init_space(file, new_dset, space) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy dataspace")
+
+ /* Set the dataset's checked_filters flag to enable writing */
+ new_dset->shared->checked_filters = TRUE;
+
+ /* Check if the dataset has a non-default DCPL & get important values, if so */
+ if(new_dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT) {
+ H5D_layout_t *layout; /* Dataset's layout information */
+ H5O_pline_t *pline; /* Dataset's I/O pipeline information */
+ H5O_fill_t *fill; /* Dataset's fill value info */
+
+ /* Check if the filters in the DCPL can be applied to this dataset */
+ if(H5Z_can_apply(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0)
+ HGOTO_ERROR(H5E_ARGS, H5E_CANTINIT, NULL, "I/O filters can't operate on this dataset")
+
+ /* Make the "set local" filter callbacks for this dataset */
+ if(H5Z_set_local(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set local filter parameters")
+
+ /* Get new dataset's property list object */
+ if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(new_dset->shared->dcpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list")
+
+ /* Retrieve the properties we need */
+ pline = &new_dset->shared->dcpl_cache.pline;
+ if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, pline) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter")
+ layout = &new_dset->shared->layout.type;
+ if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, layout) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout")
+ if(pline->nused > 0 && H5D_CHUNKED != *layout)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout")
+ fill = &new_dset->shared->dcpl_cache.fill;
+ if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill value info")
+
+ /* Check if the alloc_time is the default and error out */
+ if(fill->alloc_time == H5D_ALLOC_TIME_DEFAULT)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "invalid space allocation state")
+
+ /* Don't allow compact datasets to allocate space later */
+ if(*layout == H5D_COMPACT && fill->alloc_time != H5D_ALLOC_TIME_EARLY)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset must have early space allocation")
+
+ /* If MPI VFD is used, no filter support yet. */
+ if(IS_H5FD_MPI(file) && pline->nused > 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet")
+
+ /* Chunked datasets are non-default, so retrieve their info here */
+ if(H5P_get(dc_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk dimensions")
+
+ /* Get the dataset's external file list information */
+ if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &new_dset->shared->dcpl_cache.efl) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list")
+ } /* end if */
+
+ /* Set the latest version of the pline & fill messages, if requested */
+ if(H5F_USE_LATEST_FORMAT(file)) {
+ /* Set the latest version for the I/O pipeline message */
+ if(H5Z_set_latest_version(&new_dset->shared->dcpl_cache.pline) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of I/O filter pipeline")
+
+ /* Set the latest version for the fill value message */
+ if(H5O_fill_set_latest_version(&new_dset->shared->dcpl_cache.fill) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of fill value")
+ } /* end if */
+
+ /* Check if this dataset is going into a parallel file and set space allocation time */
+ if(IS_H5FD_MPI(file))
+ new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY;
+
+ switch(new_dset->shared->layout.type) {
+ case H5D_CONTIGUOUS:
+ {
+ hssize_t tmp_size; /* Temporary holder for raw data size */
+ hsize_t dim[H5O_LAYOUT_NDIMS]; /* Current size of data in elements */
+ hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */
+
+ /*
+ * The maximum size of the dataset cannot exceed the storage size.
+ * Also, only the slowest varying dimension of a simple data space
+ * can be extendible (currently only for external data storage).
+ */
+ new_dset->shared->layout.u.contig.addr = HADDR_UNDEF; /* Initialize to no address */
+
+ if((ndims = H5S_get_simple_extent_dims(new_dset->shared->space, dim, max_dim)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize contiguous storage")
+ for(i = 1; i < ndims; i++)
+ if(max_dim[i] > dim[i])
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible")
+ if(new_dset->shared->dcpl_cache.efl.nused > 0) {
+ hsize_t max_points = H5S_get_npoints_max(new_dset->shared->space);
+ hsize_t max_storage = H5O_efl_total_size(&new_dset->shared->dcpl_cache.efl);
+
+ if(H5S_UNLIMITED == max_points) {
+ if(H5O_EFL_UNLIMITED != max_storage)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unlimited data space but finite storage")
+ } else if(max_points * H5T_get_size(type) < max_points) {
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space * type size overflowed")
+ } else if(max_points * H5T_get_size(type) > max_storage) {
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space size exceeds external storage size")
+ }
+
+ /* Set the I/O functions for this layout type */
+ new_dset->shared->io_ops.readvv = H5D_efl_readvv;
+ new_dset->shared->io_ops.writevv = H5D_efl_writevv;
+ } /* end if */
+ else {
+ if(ndims > 0 && max_dim[0] > dim[0])
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset")
+
+ /* Set the I/O functions for this layout type */
+ new_dset->shared->io_ops.readvv = H5D_contig_readvv;
+ new_dset->shared->io_ops.writevv = H5D_contig_writevv;
+ } /* end else */
+
+ /* Compute the total size of a chunk */
+ tmp_size = H5S_GET_EXTENT_NPOINTS(new_dset->shared->space) * H5T_get_size(new_dset->shared->type);
+ H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t);
+
+ /* Get the sieve buffer size for this dataset */
+ new_dset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(file);
+ } /* end case */
+ break;
+
+ case H5D_CHUNKED:
+ {
+ hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */
+
+ /* Set up layout information */
+ if((ndims = H5S_GET_EXTENT_NDIMS(new_dset->shared->space)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "unable to get rank")
+ new_dset->shared->layout.u.chunk.ndims = (unsigned)ndims + 1;
+ HDassert((unsigned)(new_dset->shared->layout.u.chunk.ndims) <= NELMTS(new_dset->shared->layout.u.chunk.dim));
+
+ /* Initialize to no address */
+ new_dset->shared->layout.u.chunk.addr = HADDR_UNDEF;
+
+ /*
+ * Chunked storage allows any type of data space extension, so we
+ * don't even bother checking.
+ */
+ if(chunk_ndims != (unsigned)ndims)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space")
+ if(new_dset->shared->dcpl_cache.efl.nused > 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout")
+
+ /*
+ * The chunk size of a dimension with a fixed size cannot exceed
+ * the maximum dimension size
+ */
+ if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, new_dset->shared->layout.u.chunk.dim) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size")
+ new_dset->shared->layout.u.chunk.dim[new_dset->shared->layout.u.chunk.ndims-1] = H5T_get_size(new_dset->shared->type);
+
+ if(H5S_get_simple_extent_dims(new_dset->shared->space, NULL, max_dim) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions")
+ for(u = 0; u < new_dset->shared->layout.u.chunk.ndims - 1; u++)
+ if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < new_dset->shared->layout.u.chunk.dim[u])
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions")
+
+ /* Compute the total size of a chunk */
+ for(u = 1, new_dset->shared->layout.u.chunk.size = new_dset->shared->layout.u.chunk.dim[0]; u < new_dset->shared->layout.u.chunk.ndims; u++)
+ new_dset->shared->layout.u.chunk.size *= new_dset->shared->layout.u.chunk.dim[u];
+
+ /* Set the I/O functions for this layout type */
+ new_dset->shared->io_ops.readvv = H5D_istore_readvv;
+ new_dset->shared->io_ops.writevv = H5D_istore_writevv;
+
+ /* Initialize the chunk cache for the dataset */
+ if(H5D_istore_init(file, new_dset) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize chunk cache")
+
+ /* Indicate that the chunk information was initialized */
+ chunk_init = TRUE;
+ } /* end case */
+ break;
+
+ case H5D_COMPACT:
+ {
+ hssize_t tmp_size; /* Temporary holder for raw data size */
+ hsize_t comp_data_size;
+
+ /*
+ * Compact dataset is stored in dataset object header message of
+ * layout.
+ */
+ tmp_size = H5S_GET_EXTENT_NPOINTS(space) * H5T_get_size(new_dset->shared->type);
+ H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.compact.size, tmp_size, hssize_t, size_t);
+
+ /* Verify data size is smaller than maximum header message size
+ * (64KB) minus other layout message fields.
+ */
+ comp_data_size = H5O_MESG_MAX_SIZE - H5O_layout_meta_size(file, &(new_dset->shared->layout));
+ if(new_dset->shared->layout.u.compact.size > comp_data_size)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size")
+
+ /* Set the I/O functions for this layout type */
+ new_dset->shared->io_ops.readvv = H5D_compact_readvv;
+ new_dset->shared->io_ops.writevv = H5D_compact_writevv;
+ } /* end case */
+ break;
+
+ default:
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet")
+ } /* end switch */ /*lint !e788 All appropriate cases are covered */
+
+ /* Update the dataset's object header info. */
+ if(H5D_update_oh_info(file, dxpl_id, new_dset) != SUCCEED)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache")
+
+ /* Add the dataset to the list of opened objects in the file */
+ if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count")
+ if(H5FO_insert(new_dset->oloc.file, new_dset->oloc.addr, new_dset->shared, TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects")
+
+ new_dset->shared->fo_count = 1;
+
+ /* Success */
+ ret_value = new_dset;
+
+done:
+ if(!ret_value && new_dset && new_dset->shared) {
+ if(new_dset->shared) {
+ if(new_dset->shared->layout.type == H5D_CHUNKED && chunk_init) {
+ if(H5D_istore_dest(new_dset,H5AC_dxpl_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy chunk cache")
+ } /* end if */
+ if(new_dset->shared->space) {
+ if(H5S_close(new_dset->shared->space) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace")
+ } /* end if */
+ if(new_dset->shared->type) {
+ if(H5I_dec_ref(new_dset->shared->type_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype")
+ } /* end if */
+ if(H5F_addr_defined(new_dset->oloc.addr)) {
+ if(H5O_close(&(new_dset->oloc)) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header")
+ if(file) {
+ if(H5O_delete(file, dxpl_id, new_dset->oloc.addr) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTDELETE, NULL, "unable to delete object header")
+ } /* end if */
+ } /* end if */
+ if(new_dset->shared->dcpl_id != 0) {
+ if(H5I_dec_ref(new_dset->shared->dcpl_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list")
+ } /* end if */
+ H5FL_FREE(H5D_shared_t, new_dset->shared);
+ } /* end if */
+ new_dset->oloc.file = NULL;
+ H5FL_FREE(H5D_t, new_dset);
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_create() */
+
+
+/*
+ *-------------------------------------------------------------------------
+ * Function: H5D_open
+ *
+ * Purpose: Checks if dataset is already open, or opens a dataset for
+ * access.
+ *
+ * Return: Success: Dataset ID
+ * Failure: FAIL
+ *
+ * Programmer: Quincey Koziol
+ * Friday, December 20, 2002
+ *
+ *-------------------------------------------------------------------------
+ */
+H5D_t *
+H5D_open(const H5G_loc_t *loc, hid_t dxpl_id)
+{
+ H5D_shared_t *shared_fo = NULL;
+ H5D_t *dataset = NULL;
+ H5D_t *ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_open, NULL)
+
+ /* check args */
+ HDassert(loc);
+
+ /* Allocate the dataset structure */
+ if(NULL == (dataset = H5FL_CALLOC(H5D_t)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
+
+ /* Shallow copy (take ownership) of the object location object */
+ if(H5O_loc_copy(&(dataset->oloc), loc->oloc, H5_COPY_SHALLOW) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy object location")
+
+ /* Shallow copy (take ownership) of the group hier. path */
+ if(H5G_name_copy(&(dataset->path), loc->path, H5_COPY_SHALLOW) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy path")
+
+ /* Check if dataset was already open */
+ if((shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr)) == NULL) {
+ /* Clear any errors from H5FO_opened() */
+ H5E_clear_stack(NULL);
+
+ /* Open the dataset object */
+ if(H5D_open_oid(dataset, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found")
+
+ /* Add the dataset to the list of opened objects in the file */
+ if(H5FO_insert(dataset->oloc.file, dataset->oloc.addr, dataset->shared, FALSE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects")
+
+ /* Increment object count for the object in the top file */
+ if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count")
+
+ /* We're the first dataset to use the the shared info */
+ dataset->shared->fo_count = 1;
+ } /* end if */
+ else {
+ /* Point to shared info */
+ dataset->shared = shared_fo;
+
+ /* Increment # of datasets using shared information */
+ shared_fo->fo_count++;
+
+ /* Check if the object has been opened through the top file yet */
+ if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) {
+ /* Open the object through this top file */
+ if(H5O_open(&(dataset->oloc)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open object header")
+ } /* end if */
+
+ /* Increment object count for the object in the top file */
+ if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count")
+ } /* end else */
+
+ ret_value = dataset;
+
+done:
+ if(ret_value == NULL) {
+ /* Free the location--casting away const*/
+ if(dataset) {
+ if(shared_fo == NULL) /* Need to free shared fo */
+ H5FL_FREE(H5D_shared_t, dataset->shared);
+
+ H5O_loc_free(&(dataset->oloc));
+ H5G_name_free(&(dataset->path));
+
+ H5FL_FREE(H5D_t, dataset);
+ }
+ if(shared_fo)
+ shared_fo->fo_count--;
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_open() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_open_oid
+ *
+ * Purpose: Opens a dataset for access.
+ *
+ * Return: Dataset pointer on success, NULL on failure
+ *
+ * Programmer: Quincey Koziol
+ * Monday, October 12, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_open_oid(H5D_t *dataset, hid_t dxpl_id)
+{
+ H5P_genplist_t *plist; /* Property list */
+ H5O_pline_t *pline; /* I/O pipeline information */
+ H5O_fill_t *fill_prop; /* Pointer to dataset's fill value info */
+ unsigned alloc_time_state; /* Allocation time state */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_open_oid)
+
+ /* check args */
+ HDassert(dataset);
+
+ /* (Set the 'vl_type' parameter to FALSE since it doesn't matter from here) */
+ if(NULL == (dataset->shared = H5D_new(H5P_DATASET_CREATE_DEFAULT, FALSE, FALSE)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
+
+ /* Open the dataset object */
+ if(H5O_open(&(dataset->oloc)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open")
+
+ /* Get the type and space */
+ if(NULL == (dataset->shared->type = (H5T_t *)H5O_msg_read(&(dataset->oloc), H5O_DTYPE_ID, NULL, dxpl_id)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load type info from dataset header")
+ if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc), dxpl_id)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load space info from dataset header")
+
+ /* Get a datatype ID for the dataset's datatype */
+ if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type")
+
+ /* Get dataset creation property list object */
+ if(NULL == (plist = (H5P_genplist_t *)H5I_object(dataset->shared->dcpl_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list")
+
+ /* Get the optional filters message */
+ pline = &dataset->shared->dcpl_cache.pline;
+ if(NULL != H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, pline, dxpl_id)) {
+ if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, pline) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set pipeline")
+ } /* end if */
+ else
+ H5E_clear_stack(NULL);
+
+ /*
+ * Get the raw data layout info. It's actually stored in two locations:
+ * the storage message of the dataset (dataset->storage) and certain
+ * values are copied to the dataset create plist so the user can query
+ * them.
+ */
+ if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message")
+ if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->shared->layout.type) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout")
+ switch(dataset->shared->layout.type) {
+ case H5D_CONTIGUOUS:
+ /* Compute the size of the contiguous storage for versions of the
+ * layout message less than version 3 because versions 1 & 2 would
+ * truncate the dimension sizes to 32-bits of information. - QAK 5/26/04
+ */
+ if(dataset->shared->layout.version < 3) {
+ hssize_t tmp_size; /* Temporary holder for raw data size */
+
+ tmp_size = H5S_GET_EXTENT_NPOINTS(dataset->shared->space) * H5T_get_size(dataset->shared->type);
+ H5_ASSIGN_OVERFLOW(dataset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t);
+ } /* end if */
+
+ /* Set the I/O functions for this layout type */
+ dataset->shared->io_ops.readvv = H5D_contig_readvv;
+ dataset->shared->io_ops.writevv = H5D_contig_writevv;
+
+ /* Get the sieve buffer size for this dataset */
+ dataset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(dataset->oloc.file);
+ break;
+
+ case H5D_CHUNKED:
+ /*
+ * Chunked storage. The creation plist's dimension is one less than
+ * the chunk dimension because the chunk includes a dimension for the
+ * individual bytes of the datatype.
+ */
+ {
+ unsigned chunk_ndims; /* Dimensionality of chunk */
+
+ chunk_ndims = dataset->shared->layout.u.chunk.ndims - 1;
+
+ if(H5P_set(plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk dimensions")
+ if(H5P_set(plist, H5D_CRT_CHUNK_SIZE_NAME, dataset->shared->layout.u.chunk.dim) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk size")
+
+ /* Initialize the chunk cache for the dataset */
+ if(H5D_istore_init(dataset->oloc.file, dataset) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache")
+ }
+
+ /* Set the I/O functions for this layout type */
+ dataset->shared->io_ops.readvv = H5D_istore_readvv;
+ dataset->shared->io_ops.writevv = H5D_istore_writevv;
+ break;
+
+ case H5D_COMPACT:
+ /* Set the I/O functions for this layout type */
+ dataset->shared->io_ops.readvv = H5D_compact_readvv;
+ dataset->shared->io_ops.writevv = H5D_compact_writevv;
+ break;
+
+ default:
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet")
+ } /* end switch */ /*lint !e788 All appropriate cases are covered */
+
+ /* Point at dataset's copy, to cache it for later */
+ fill_prop = &dataset->shared->dcpl_cache.fill;
+
+ /* Try to get the new fill value message from the object header */
+ if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_NEW_ID, fill_prop, dxpl_id)) {
+ H5E_clear_stack(NULL);
+
+ /* For backward compatibility, try to retrieve the old fill value message */
+ if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_ID, fill_prop, dxpl_id)) {
+ H5E_clear_stack(NULL);
+
+ /* Set the space allocation time appropriately, based on the type of dataset storage */
+ switch(dataset->shared->layout.type) {
+ case H5D_COMPACT:
+ fill_prop->alloc_time = H5D_ALLOC_TIME_EARLY;
+ break;
+
+ case H5D_CONTIGUOUS:
+ fill_prop->alloc_time = H5D_ALLOC_TIME_LATE;
+ break;
+
+ case H5D_CHUNKED:
+ fill_prop->alloc_time = H5D_ALLOC_TIME_INCR;
+ break;
+
+ default:
+ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet")
+ } /* end switch */ /*lint !e788 All appropriate cases are covered */
+ } /* end if */
+
+ /* If "old" fill value size is 0 (undefined), map it to -1 */
+ if(fill_prop->size == 0)
+ fill_prop->size = (size_t)-1;
+ } /* end if */
+ alloc_time_state = 0;
+ if((dataset->shared->layout.type == H5D_COMPACT && fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY)
+ || (dataset->shared->layout.type == H5D_CONTIGUOUS && fill_prop->alloc_time == H5D_ALLOC_TIME_LATE)
+ || (dataset->shared->layout.type == H5D_CHUNKED && fill_prop->alloc_time == H5D_ALLOC_TIME_INCR))
+ alloc_time_state = 1;
+
+ /* Set revised fill value properties, if they are different from the defaults */
+ if(H5P_fill_value_cmp(&H5D_def_dset.dcpl_cache.fill, fill_prop, sizeof(H5O_fill_t))) {
+ if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set fill value")
+ if(H5P_set(plist, H5D_CRT_ALLOC_TIME_STATE_NAME, &alloc_time_state) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set allocation time state")
+ } /* end if */
+
+ /* Get the external file list message, which might not exist. Space is
+ * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */
+ if((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
+ || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) {
+ if(NULL != H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id)) {
+ if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list")
+
+ /* Override the I/O functions for this layout type */
+ dataset->shared->io_ops.readvv = H5D_efl_readvv;
+ dataset->shared->io_ops.writevv = H5D_efl_writevv;
+ } /* end if */
+ else
+ H5E_clear_stack(NULL);
+ } /* end if */
+
+ /*
+ * Make sure all storage is properly initialized.
+ * This is important only for parallel I/O where the space must
+ * be fully allocated before I/O can happen.
+ */
+ if((H5F_get_intent(dataset->oloc.file) & H5F_ACC_RDWR)
+ && ((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr))
+ || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))
+ && IS_H5FD_MPI(dataset->oloc.file)) {
+ if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_OPEN, TRUE, FALSE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage")
+ } /* end if */
+
+done:
+ if(ret_value < 0) {
+ if(H5F_addr_defined(dataset->oloc.addr)) {
+ if(H5O_close(&(dataset->oloc)) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header")
+ } /* end if */
+ if(dataset->shared->space) {
+ if(H5S_close(dataset->shared->space) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace")
+ } /* end if */
+ if(dataset->shared->type) {
+ if(dataset->shared->type_id > 0) {
+ if(H5I_dec_ref(dataset->shared->type_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype")
+ } /* end if */
+ else {
+ if(H5T_close(dataset->shared->type) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype")
+ } /* end else */
+ } /* end if */
+ } /* end if */
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_open_oid() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_close
+ *
+ * Purpose: Insures that all data has been saved to the file, closes the
+ * dataset object header, and frees all resources used by the
+ * descriptor.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Thursday, December 4, 1997
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_close(H5D_t *dataset)
+{
+ unsigned free_failed = FALSE;
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_close, FAIL)
+
+ /* check args */
+ HDassert(dataset && dataset->oloc.file && dataset->shared);
+ HDassert(dataset->shared->fo_count >0);
+
+ /* Dump debugging info */
+#ifdef H5D_ISTORE_DEBUG
+ H5D_istore_stats(dataset, FALSE);
+#endif /* H5F_ISTORE_DEBUG */
+
+ dataset->shared->fo_count--;
+ if(dataset->shared->fo_count == 0) {
+ /* Free the data sieve buffer, if it's been allocated */
+ if(dataset->shared->cache.contig.sieve_buf) {
+ HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */
+
+ /* Flush the raw data buffer, if its dirty */
+ if(dataset->shared->cache.contig.sieve_dirty) {
+ /* Write dirty data sieve buffer to file */
+ if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc,
+ dataset->shared->cache.contig.sieve_size, H5AC_dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed")
+
+ /* Reset sieve buffer dirty flag */
+ dataset->shared->cache.contig.sieve_dirty = FALSE;
+ } /* end if */
+
+ dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf);
+ } /* end if */
+
+ /* Free cached information for each kind of dataset */
+ switch(dataset->shared->layout.type) {
+ case H5D_CONTIGUOUS:
+ break;
+
+ case H5D_CHUNKED:
+ /* Flush and destroy chunks in the cache */
+ if(H5D_istore_dest(dataset,H5AC_dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache")
+ break;
+
+ case H5D_COMPACT:
+ /* Update header message of layout for compact dataset. */
+ if(dataset->shared->layout.u.compact.dirty) {
+ if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), H5AC_dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to update layout message")
+ dataset->shared->layout.u.compact.dirty = FALSE;
+ } /* end if */
+
+ /* Free the buffer for the raw data for compact datasets */
+ dataset->shared->layout.u.compact.buf = H5MM_xfree(dataset->shared->layout.u.compact.buf);
+ break;
+
+ default:
+ HDassert("not implemented yet" && 0);
+#ifdef NDEBUG
+ HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout")
+#endif /* NDEBUG */
+ } /* end switch */ /*lint !e788 All appropriate cases are covered */
+
+ /*
+ * Release datatype, dataspace and creation property list -- there isn't
+ * much we can do if one of these fails, so we just continue.
+ */
+ free_failed = (H5I_dec_ref(dataset->shared->type_id) < 0 || H5S_close(dataset->shared->space) < 0 ||
+ H5I_dec_ref(dataset->shared->dcpl_id) < 0);
+
+ /* Remove the dataset from the list of opened objects in the file */
+ if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object")
+ if(H5FO_delete(dataset->oloc.file, H5AC_dxpl_id, dataset->oloc.addr) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't remove dataset from list of open objects")
+
+ /* Close the dataset object */
+ /* (This closes the file, if this is the last object open) */
+ if(H5O_close(&(dataset->oloc)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header")
+
+ /*
+ * Free memory. Before freeing the memory set the file pointer to NULL.
+ * We always check for a null file pointer in other H5D functions to be
+ * sure we're not accessing an already freed dataset (see the HDassert()
+ * above).
+ */
+ dataset->oloc.file = NULL;
+
+ H5FL_FREE(H5D_shared_t, dataset->shared);
+ } /* end if */
+ else {
+ /* Decrement the ref. count for this object in the top file */
+ if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object")
+
+ /* Check reference count for this object in the top file */
+ if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0)
+ if(H5O_close(&(dataset->oloc)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to close")
+ } /* end else */
+
+ /* Release the dataset's path info */
+ if(H5G_name_free(&(dataset->path)) < 0)
+ free_failed = TRUE;
+
+ /* Free the dataset's memory structure */
+ H5FL_FREE(H5D_t, dataset);
+
+ /* Check if anything failed in the middle... */
+ if(free_failed)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free a component of the dataset, but the dataset was freed anyway.")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_close() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_oloc
+ *
+ * Purpose: Returns a pointer to the object location for a dataset.
+ *
+ * Return: Success: Ptr to location
+ * Failure: NULL
+ *
+ * Programmer: Robb Matzke
+ * Friday, April 24, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+H5O_loc_t *
+H5D_oloc(H5D_t *dataset)
+{
+ /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_oloc)
+
+ FUNC_LEAVE_NOAPI(dataset ? &(dataset->oloc) : (H5O_loc_t *)NULL)
+} /* end H5D_oloc() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_nameof
+ *
+ * Purpose: Returns a pointer to the group hier. path for a dataset.
+ *
+ * Return: Success: Ptr to entry
+ * Failure: NULL
+ *
+ * Programmer: Quincey Koziol
+ * Monday, September 12, 2005
+ *
+ *-------------------------------------------------------------------------
+ */
+H5G_name_t *
+H5D_nameof(H5D_t *dataset)
+{
+ /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_nameof)
+
+ FUNC_LEAVE_NOAPI(dataset ? &(dataset->path) : (H5G_name_t *)NULL)
+} /* end H5D_nameof() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_typeof
+ *
+ * Purpose: Returns a pointer to the dataset's datatype. The datatype
+ * is not copied.
+ *
+ * Return: Success: Ptr to the dataset's datatype, uncopied.
+ *
+ * Failure: NULL
+ *
+ * Programmer: Robb Matzke
+ * Thursday, June 4, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+H5T_t *
+H5D_typeof(const H5D_t *dset)
+{
+ /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_typeof)
+
+ HDassert(dset);
+ HDassert(dset->shared->type);
+
+ FUNC_LEAVE_NOAPI(dset->shared->type)
+} /* end H5D_typeof() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_get_file
+ *
+ * Purpose: Returns the dataset's file pointer.
+ *
+ * Return: Success: Ptr to the dataset's file pointer.
+ *
+ * Failure: NULL
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, October 22, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+static H5F_t *
+H5D_get_file(const H5D_t *dset)
+{
+ /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_get_file)
+
+ HDassert(dset);
+ HDassert(dset->oloc.file);
+
+ FUNC_LEAVE_NOAPI(dset->oloc.file)
+} /* end H5D_get_file() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_alloc_storage
+ *
+ * Purpose: Allocate storage for the raw data of a dataset.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Friday, January 16, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc,
+ hbool_t update_time, hbool_t full_overwrite)
+{
+ struct H5O_layout_t *layout; /* The dataset's layout information */
+ hbool_t must_init_space = FALSE; /* Flag to indicate that space should be initialized */
+ hbool_t addr_set = FALSE; /* Flag to indicate that the dataset's storage address was set */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_alloc_storage)
+
+ /* check args */
+ HDassert(f);
+ HDassert(dset);
+
+ /* If the data is stored in external files, don't set an address for the layout
+ * We assume that external storage is already
+ * allocated by the caller, or at least will be before I/O is performed.
+ */
+ if(!(H5S_NULL == H5S_GET_EXTENT_TYPE(dset->shared->space) || dset->shared->dcpl_cache.efl.nused > 0)) {
+ /* Get a pointer to the dataset's layout information */
+ layout = &(dset->shared->layout);
+
+ switch(layout->type) {
+ case H5D_CONTIGUOUS:
+ if(!H5F_addr_defined(layout->u.contig.addr)) {
+ /* Reserve space in the file for the entire array */
+ if(H5D_contig_create(f, dxpl_id, layout/*out*/) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage")
+
+ /* Indicate that we set the storage addr */
+ addr_set = TRUE;
+
+ /* Indicate that we should initialize storage space */
+ must_init_space = TRUE;
+ } /* end if */
+ break;
+
+ case H5D_CHUNKED:
+ if(!H5F_addr_defined(layout->u.chunk.addr)) {
+ /* Create the root of the B-tree that describes chunked storage */
+ if(H5D_istore_create(f, dxpl_id, layout/*out*/) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage")
+
+ /* Indicate that we set the storage addr */
+ addr_set = TRUE;
+
+ /* Indicate that we should initialize storage space */
+ must_init_space = TRUE;
+ } /* end if */
+
+ /* If space allocation is set to 'early' and we are extending
+ * the dataset, indicate that space should be allocated, so the
+ * B-tree gets expanded. -QAK
+ */
+ if(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY
+ && time_alloc == H5D_ALLOC_EXTEND)
+ must_init_space = 1;
+ break;
+
+ case H5D_COMPACT:
+ /* Check if space is already allocated */
+ if(layout->u.compact.buf==NULL) {
+ /* Reserve space in layout header message for the entire array. */
+ HDassert(layout->u.compact.size > 0);
+ if(NULL == (layout->u.compact.buf = H5MM_malloc(layout->u.compact.size)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset")
+ if(!full_overwrite)
+ HDmemset(layout->u.compact.buf, 0, layout->u.compact.size);
+ layout->u.compact.dirty = TRUE;
+
+ /* Indicate that we set the storage addr */
+ addr_set = TRUE;
+
+ /* Indicate that we should initialize storage space */
+ must_init_space = TRUE;
+ } /* end if */
+ break;
+
+ default:
+ HDassert("not implemented yet" && 0);
+#ifdef NDEBUG
+ HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout")
+#endif /* NDEBUG */
+ } /* end switch */ /*lint !e788 All appropriate cases are covered */
+
+ /* Check if we need to initialize the space */
+ if(must_init_space) {
+ if(layout->type == H5D_CHUNKED) {
+ /* If we are doing incremental allocation and the B-tree got
+ * created during a H5Dwrite call, don't initialize the storage
+ * now, wait for the actual writes to each block and let the
+ * low-level chunking routines handle initialize the fill-values.
+ * Otherwise, pass along the space initialization call and let
+ * the low-level chunking routines sort out whether to write
+ * fill values to the chunks they allocate space for. Yes,
+ * this is icky. -QAK
+ */
+ if(!(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_INCR && time_alloc == H5D_ALLOC_WRITE))
+ if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value")
+ } /* end if */
+ else {
+ H5D_fill_value_t fill_status; /* The fill value status */
+
+ /* Check the dataset's fill-value status */
+ if(H5P_is_fill_value_defined(&dset->shared->dcpl_cache.fill, &fill_status) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined")
+
+ /* If we are filling the dataset on allocation or "if set" and
+ * the fill value _is_ set, do that now */
+ if(dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC ||
+ (dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
+ if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value")
+ } /* end if */
+ } /* end else */
+ } /* end if */
+
+ /* Also update header message for layout with new address, if we
+ * set the address. (this is improves forward compatibility).
+ */
+ if(time_alloc != H5D_ALLOC_CREATE && addr_set)
+ if(H5O_msg_write(&dset->oloc, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_time, &dset->shared->layout, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message")
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_alloc_storage() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_init_storage
+ *
+ * Purpose: Initialize the data for a new dataset. If a selection is
+ * defined for SPACE then initialize only that part of the
+ * dataset.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Robb Matzke
+ * Monday, October 5, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id)
+{
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_init_storage)
+
+ HDassert(dset);
+
+ switch (dset->shared->layout.type) {
+ case H5D_COMPACT:
+ /* If we will be immediately overwriting the values, don't bother to clear them */
+ if(!full_overwrite) {
+ /* Fill the compact dataset storage */
+ if(H5D_compact_fill(dset, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize compact dataset storage")
+ } /* end if */
+ break;
+
+ case H5D_CONTIGUOUS:
+ /* Don't write default fill values to external files */
+ /* If we will be immediately overwriting the values, don't bother to clear them */
+ if((dset->shared->dcpl_cache.efl.nused == 0 || dset->shared->dcpl_cache.fill.buf) && !full_overwrite)
+ if(H5D_contig_fill(dset, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset")
+ break;
+
+ case H5D_CHUNKED:
+ /*
+ * Allocate file space
+ * for all chunks now and initialize each chunk with the fill value.
+ */
+ if(H5D_istore_allocate(dset, dxpl_id, full_overwrite) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset")
+ break;
+
+ default:
+ HDassert("not implemented yet" && 0);
+#ifdef NDEBUG
+ HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout")
+#endif /* NDEBUG */
+ } /* end switch */ /*lint !e788 All appropriate cases are covered */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_init_storage() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_get_storage_size
+ *
+ * Purpose: Determines how much space has been reserved to store the raw
+ * data of a dataset.
+ *
+ * Return: Success: Number of bytes reserved to hold raw data.
+ *
+ * Failure: 0
+ *
+ * Programmer: Robb Matzke
+ * Wednesday, April 21, 1999
+ *
+ *-------------------------------------------------------------------------
+ */
+hsize_t
+H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id)
+{
+ hsize_t ret_value;
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_get_storage_size)
+
+ switch(dset->shared->layout.type) {
+ case H5D_CHUNKED:
+ if(dset->shared->layout.u.chunk.addr == HADDR_UNDEF)
+ ret_value = 0;
+ else
+ ret_value = H5D_istore_allocated(dset, dxpl_id);
+ break;
+
+ case H5D_CONTIGUOUS:
+ /* Datasets which are not allocated yet are using no space on disk */
+ if(dset->shared->layout.u.contig.addr == HADDR_UNDEF)
+ ret_value = 0;
+ else
+ ret_value = dset->shared->layout.u.contig.size;
+ break;
+
+ case H5D_COMPACT:
+ ret_value = dset->shared->layout.u.compact.size;
+ break;
+
+ default:
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset type")
+ } /*lint !e788 All appropriate cases are covered */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_get_storage_size() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_get_offset
+ *
+ * Purpose: Private function for H5D_get_offset. Returns the address
+ * of dataset in file.
+ *
+ * Return: Success: the address of dataset
+ *
+ * Failure: HADDR_UNDEF
+ *
+ * Programmer: Raymond Lu
+ * November 6, 2002
+ *
+ *-------------------------------------------------------------------------
+ */
+haddr_t
+H5D_get_offset(const H5D_t *dset)
+{
+ haddr_t base_addr;
+ H5F_t *f;
+ haddr_t ret_value = HADDR_UNDEF;
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_get_offset)
+
+ HDassert(dset);
+
+ switch(dset->shared->layout.type) {
+ case H5D_CHUNKED:
+ case H5D_COMPACT:
+ break;
+
+ case H5D_CONTIGUOUS:
+ /* If dataspace hasn't been allocated or dataset is stored in
+ * an external file, the value will be HADDR_UNDEF. */
+ f = H5D_get_file(dset);
+ base_addr = H5F_get_base_addr(f);
+
+ /* If there's user block in file, returns the absolute dataset offset
+ * from the beginning of file. */
+ if(base_addr != HADDR_UNDEF)
+ ret_value = dset->shared->layout.u.contig.addr + base_addr;
+ else
+ ret_value = dset->shared->layout.u.contig.addr;
+ break;
+
+ default:
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "unknown dataset layout type")
+ } /*lint !e788 All appropriate cases are covered */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_get_offset() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_iterate
+ *
+ * Purpose: Internal version of H5Diterate()
+ *
+ * Return: Returns the return value of the last operator if it was non-zero,
+ * or zero if all elements were processed. Otherwise returns a
+ * negative value.
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, November 22, 2005
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t op,
+ void *operator_data)
+{
+ herr_t ret_value;
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_iterate)
+
+ /* Check args */
+ HDassert(buf);
+ HDassert(H5I_DATATYPE == H5I_get_type(type_id));
+ HDassert(space);
+ HDassert(H5S_has_extent(space));
+ HDassert(op);
+
+ ret_value = H5S_select_iterate(buf, type_id, space, op, operator_data);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_iterate() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_vlen_reclaim
+ *
+ * Purpose: Frees the buffers allocated for storing variable-length data
+ * in memory. Only frees the VL data in the selection defined in the
+ * dataspace. The dataset transfer property list is required to find the
+ * correct allocation/free methods for the VL data in the buffer.
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, November 22, 2005
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_vlen_reclaim(hid_t type_id, H5S_t *space, hid_t plist_id, void *buf)
+{
+ H5T_vlen_alloc_info_t _vl_alloc_info; /* VL allocation info buffer */
+ H5T_vlen_alloc_info_t *vl_alloc_info = &_vl_alloc_info; /* VL allocation info */
+ herr_t ret_value;
+
+ FUNC_ENTER_NOAPI(H5D_vlen_reclaim, FAIL)
+
+ /* Check args */
+ HDassert(H5I_DATATYPE == H5I_get_type(type_id));
+ HDassert(space);
+ HDassert(H5P_isa_class(plist_id, H5P_DATASET_XFER));
+ HDassert(buf);
+
+ /* Get the allocation info */
+ if(H5T_vlen_get_alloc_info(plist_id,&vl_alloc_info) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "unable to retrieve VL allocation info")
+
+ /* Call H5D_iterate with args, etc. */
+ ret_value = H5D_iterate(buf, type_id, space ,H5T_vlen_reclaim, vl_alloc_info);
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_vlen_reclaim() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_vlen_get_buf_size_alloc
+ *
+ * Purpose: This routine makes certain there is enough space in the temporary
+ * buffer for the new data to read in. All the VL data read in is actually
+ * placed in this buffer, overwriting the previous data. Needless to say,
+ * this data is not actually usable.
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, August 17, 1999
+ *
+ *-------------------------------------------------------------------------
+ */
+void *
+H5D_vlen_get_buf_size_alloc(size_t size, void *info)
+{
+ H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)info;
+ void *ret_value; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_vlen_get_buf_size_alloc)
+
+ /* Get a temporary pointer to space for the VL data */
+ if((vlen_bufsize->vl_tbuf = H5FL_BLK_REALLOC(vlen_vl_buf, vlen_bufsize->vl_tbuf, size)) != NULL)
+ vlen_bufsize->size += size;
+
+ /* Set return value */
+ ret_value = vlen_bufsize->vl_tbuf;
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_vlen_get_buf_size_alloc() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_vlen_get_buf_size
+ *
+ * Purpose: This routine checks the number of bytes required to store a single
+ * element from a dataset in memory, creating a selection with just the
+ * single element selected to read in the element and using a custom memory
+ * allocator for any VL data encountered.
+ * The *size value is modified according to how many bytes are
+ * required to store the element in memory.
+ *
+ * Implementation: This routine actually performs the read with a custom
+ * memory manager which basically just counts the bytes requested and
+ * uses a temporary memory buffer (through the H5FL API) to make certain
+ * enough space is available to perform the read. Then the temporary
+ * buffer is released and the number of bytes allocated is returned.
+ * Kinda kludgy, but easier than the other method of trying to figure out
+ * the sizes without actually reading the data in... - QAK
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Tuesday, August 17, 1999
+ *
+ *-------------------------------------------------------------------------
+ */
+/* ARGSUSED */
+herr_t
+H5D_vlen_get_buf_size(void UNUSED *elem, hid_t type_id, unsigned UNUSED ndim, const hsize_t *point, void *op_data)
+{
+ H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)op_data;
+ H5T_t *dt; /* Datatype for operation */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_vlen_get_buf_size)
+
+ HDassert(op_data);
+ HDassert(H5I_DATATYPE == H5I_get_type(type_id));
+
+ /* Check args */
+ if(NULL == (dt = (H5T_t *)H5I_object(type_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
+
+ /* Make certain there is enough fixed-length buffer available */
+ if(NULL == (vlen_bufsize->fl_tbuf = H5FL_BLK_REALLOC(vlen_fl_buf, vlen_bufsize->fl_tbuf, H5T_get_size(dt))))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't resize tbuf")
+
+ /* Select point to read in */
+ if(H5Sselect_elements(vlen_bufsize->fspace_id, H5S_SELECT_SET, (size_t)1, (const hsize_t **)point) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't select point")
+
+ /* Read in the point (with the custom VL memory allocator) */
+ if(H5Dread(vlen_bufsize->dataset_id, type_id, vlen_bufsize->mspace_id, vlen_bufsize->fspace_id, vlen_bufsize->xfer_pid, vlen_bufsize->fl_tbuf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point")
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_vlen_get_buf_size() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_check_filters
+ *
+ * Purpose: Check if the filters have be initialized for the dataset
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Thursday, October 11, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_check_filters(H5D_t *dataset)
+{
+ H5O_fill_t *fill; /* Dataset's fill value */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_check_filters)
+
+ /* Check args */
+ HDassert(dataset);
+
+ /* Check if the filters in the DCPL will need to encode, and if so, can they?
+ *
+ * Filters need encoding if fill value is defined and a fill policy is set
+ * that requires writing on an extend.
+ */
+ fill = &dataset->shared->dcpl_cache.fill;
+ if(!dataset->shared->checked_filters) {
+ H5D_fill_value_t fill_status; /* Whether the fill value is defined */
+
+ /* Retrieve the "defined" status of the fill value */
+ if(H5P_is_fill_value_defined(fill, &fill_status) < 0)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Couldn't retrieve fill value from dataset.")
+
+ /* See if we can check the filter status */
+ if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) {
+ if(fill->fill_time == H5D_FILL_TIME_ALLOC ||
+ (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) {
+ /* Filters must have encoding enabled. Ensure that all filters can be applied */
+ if(H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0)
+ HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters")
+
+ dataset->shared->checked_filters = TRUE;
+ } /* end if */
+ } /* end if */
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_check_filters() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_set_extent
+ *
+ * Purpose: Based on H5D_extend, allows change to a lower dimension,
+ * calls H5S_set_extent and H5D_istore_prune_by_extent instead
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ * April 9, 2002
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id)
+{
+ H5S_t *space; /* Dataset's dataspace */
+ int rank; /* Dataspace # of dimensions */
+ hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dimension sizes */
+ htri_t changed; /* Whether the dataspace changed size */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI_NOINIT(H5D_set_extent)
+
+ /* Check args */
+ HDassert(dset);
+ HDassert(size);
+
+ /* Check if the filters in the DCPL will need to encode, and if so, can they? */
+ if(H5D_check_filters(dset) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't apply filters")
+
+ /* Get the data space */
+ space = dset->shared->space;
+
+ /* Check if we are shrinking or expanding any of the dimensions */
+ if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
+
+ /* Modify the size of the data space */
+ if((changed = H5S_set_extent(space, size)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space")
+
+ /* Don't bother updating things, unless they've changed */
+ if(changed) {
+ hbool_t shrink = FALSE; /* Flag to indicate a dimension has shrank */
+ hbool_t expand = FALSE; /* Flag to indicate a dimension has grown */
+ unsigned u; /* Local index variable */
+
+ /* Determine if we are shrinking and/or expanding any dimensions */
+ for(u = 0; u < (unsigned)rank; u++) {
+ if(size[u] < curr_dims[u])
+ shrink = TRUE;
+ if(size[u] > curr_dims[u])
+ expand = TRUE;
+ } /* end for */
+
+ /*-------------------------------------------------------------------------
+ * Modify the dataset storage
+ *-------------------------------------------------------------------------
+ */
+ /* Save the new dataspace in the file if necessary */
+ if(H5S_write(&(dset->oloc), space, TRUE, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace")
+
+ /* Update the index values for the cached chunks for this dataset */
+ if(H5D_CHUNKED == dset->shared->layout.type)
+ if(H5D_istore_update_cache(dset, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices")
+
+ /* Allocate space for the new parts of the dataset, if appropriate */
+ if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY)
+ if(H5D_alloc_storage(dset->oloc.file, dxpl_id, dset, H5D_ALLOC_EXTEND, TRUE, FALSE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage")
+
+
+ /*-------------------------------------------------------------------------
+ * Remove chunk information in the case of chunked datasets
+ * This removal takes place only in case we are shrinking the dateset
+ *-------------------------------------------------------------------------
+ */
+ if(shrink && H5D_CHUNKED == dset->shared->layout.type) {
+ H5D_io_info_t io_info; /* Dataset I/O info */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Construct dataset I/O info */
+ H5D_BUILD_IO_INFO(&io_info, dset, dxpl_cache, dxpl_id, NULL);
+
+ /* Remove excess chunks */
+ if(H5D_istore_prune_by_extent(&io_info, curr_dims) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ")
+
+ /* Reset the elements outsize the new dimensions, but in existing chunks */
+ if(H5D_istore_initialize_by_extent(&io_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks ")
+ } /* end if */
+ } /* end if */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_set_extent() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D_flush
+ *
+ * Purpose: Flush any dataset information cached in memory
+ *
+ * Return: Success: Non-negative
+ * Failure: Negative
+ *
+ * Programmer: Ray Lu
+ * August 14, 2002
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D_flush(const H5F_t *f, hid_t dxpl_id, unsigned flags)
+{
+ hid_t *id_list = NULL; /* Array of dataset IDs */
+ unsigned num_dsets; /* Number of datasets in file */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_NOAPI(H5D_flush, FAIL)
+
+ /* Check args */
+ HDassert(f);
+
+ /* Retrieve the # of outstanding dataset IDs */
+ num_dsets = H5F_get_obj_count(f, H5F_OBJ_DATASET);
+
+ /* Check for something to do */
+ if(num_dsets > 0) {
+ H5D_t *dataset; /* Dataset pointer */
+ unsigned u; /* Index variable */
+
+ H5_CHECK_OVERFLOW(num_dsets, unsigned, size_t);
+ if(NULL == (id_list = (hid_t *)H5MM_malloc((size_t)num_dsets * sizeof(hid_t))))
+ HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to allocate memory for ID list")
+ if(H5F_get_obj_ids(f, H5F_OBJ_DATASET, -1, id_list) != num_dsets)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset ID list")
+
+ /* Iterate through the open datasets */
+ for(u = 0; u < num_dsets; u++) {
+ if(NULL == (dataset = (H5D_t *)H5I_object_verify(id_list[u], H5I_DATASET)))
+ HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset object")
+
+ /* 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(f, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc,
+ dataset->shared->cache.contig.sieve_size, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed")
+
+ /* Reset sieve buffer dirty flag */
+ dataset->shared->cache.contig.sieve_dirty = FALSE;
+ } /* end if */
+
+ /* Flush cached information for each kind of dataset */
+ switch(dataset->shared->layout.type) {
+ case H5D_CONTIGUOUS:
+ break;
+
+ case H5D_CHUNKED:
+ /* Flush the raw data cache */
+ if(H5D_istore_flush(dataset, dxpl_id, flags & H5F_FLUSH_INVALIDATE) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush raw data cache")
+ break;
+
+ case H5D_COMPACT:
+ if(dataset->shared->layout.u.compact.dirty) {
+ if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), dxpl_id) < 0)
+ HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message")
+ dataset->shared->layout.u.compact.dirty = FALSE;
+ } /* end if */
+ break;
+
+ default:
+ HDassert("not implemented yet" && 0);
+#ifdef NDEBUG
+ HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout")
+#endif /* NDEBUG */
+ } /* end switch */ /*lint !e788 All appropriate cases are covered */
+ } /* end for */
+ } /* end if */
+
+done:
+ if(id_list)
+ H5MM_xfree(id_list);
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D_flush() */
+