mirror/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2025-02-17 16:10:24 +08:00
Code Issues Packages Projects Releases Wiki Activity
2dae075569
hdf5/src/H5Dint.c
Quincey Koziol 41aeac4504 [svn-r26213] Description: 
Minor code cleanups, to align with revise_chunks branch.

Tested on:
    Mac OSX/64 10.10.2 (amazon) w/serial & parallel
    Linux/32 2.6.x (jam) w/serial
2015-02-18 13:25:05 -05:00

2738 lines
107 KiB
C
Raw Blame History

This file contains invisible Unicode characters

This file contains invisible Unicode characters that are indistinguishable to humans but may be processed differently by a computer. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 "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 */
/******************/
/* Struct for holding callback info during H5D_flush operation */
typedef struct {
const H5F_t *f; /* Pointer to file being flushed */
hid_t dxpl_id; /* DXPL for I/O operations */
} H5D_flush_ud_t;
/********************/
/* Local Prototypes */
/********************/
/* General stuff */
static herr_t H5D__get_dxpl_cache_real(hid_t dxpl_id, H5D_dxpl_cache_t *cache);
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,
hid_t dapl_id);
static herr_t H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id);
static herr_t H5D__init_storage(const H5D_t *dataset, hbool_t full_overwrite,
hsize_t old_dim[], 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);
/* 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 /* Callback routine for closing objects of this class */
}};
/*-------------------------------------------------------------------------
* 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(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_STATIC
/* 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")
/* 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_NOERR
if(H5_interface_initialize_g) {
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 */
else {
/* Close public interface */
n += H5D__term_pub_interface();
/* Close deprecated interface */
n += H5D__term_deprec_interface();
/* Destroy the dataset object id group */
(void)H5I_dec_type_ref(H5I_DATASET);
n++; /*H5I*/
/* Mark closed */
H5_interface_initialize_g = 0;
} /* end else */
} /* end if */
FUNC_LEAVE_NOAPI(n)
} /* end H5D_term_interface() */
/*--------------------------------------------------------------------------
NAME
H5D__get_dxpl_cache_real
PURPOSE
Get all the values for the DXPL cache.
USAGE
herr_t H5D__get_dxpl_cache_real(dxpl_id, cache)
hid_t dxpl_id; IN: DXPL to query
H5D_dxpl_cache_t *cache;IN/OUT: DXPL cache to fill with values
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Query all the values from a DXPL that are needed by internal routines
within the library.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
static herr_t
H5D__get_dxpl_cache_real(hid_t dxpl_id, H5D_dxpl_cache_t *cache)
{
H5P_genplist_t *dx_plist; /* Data transfer property list */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
/* Check args */
HDassert(cache);
/* Get the dataset transfer property list */
if(NULL == (dx_plist = (H5P_genplist_t *)H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
/* Get maximum temporary buffer size */
if(H5P_get(dx_plist, H5D_XFER_MAX_TEMP_BUF_NAME, &cache->max_temp_buf) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve maximum temporary buffer size")
/* Get temporary buffer pointer */
if(H5P_get(dx_plist, H5D_XFER_TCONV_BUF_NAME, &cache->tconv_buf) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve temporary buffer pointer")
/* Get background buffer pointer */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_NAME, &cache->bkgr_buf) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer pointer")
/* Get background buffer type */
if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &cache->bkgr_buf_type) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type")
/* Get B-tree split ratios */
if(H5P_get(dx_plist, H5D_XFER_BTREE_SPLIT_RATIO_NAME, &cache->btree_split_ratio) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve B-tree split ratios")
/* Get I/O vector size */
if(H5P_get(dx_plist, H5D_XFER_HYPER_VECTOR_SIZE_NAME, &cache->vec_size) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve I/O vector size")
#ifdef H5_HAVE_PARALLEL
/* Collect Parallel I/O information for possible later use */
if(H5P_get(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &cache->xfer_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve parallel transfer method")
if(H5P_get(dx_plist, H5D_XFER_MPIO_COLLECTIVE_OPT_NAME, &cache->coll_opt_mode) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve collective transfer option")
#endif /* H5_HAVE_PARALLEL */
/* Get error detection properties */
if(H5P_get(dx_plist, H5D_XFER_EDC_NAME, &cache->err_detect) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve error detection info")
/* Get filter callback function */
if(H5P_get(dx_plist, H5D_XFER_FILTER_CB_NAME, &cache->filter_cb) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve filter callback function")
/* Get the data transform property */
if(H5P_get(dx_plist, H5D_XFER_XFORM_NAME, &cache->data_xform_prop) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve data transform info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__get_dxpl_cache_real() */
/*--------------------------------------------------------------------------
NAME
H5D__get_dxpl_cache
PURPOSE
Get all the values for the DXPL cache.
USAGE
herr_t H5D__get_dxpl_cache(dxpl_id, cache)
hid_t dxpl_id; IN: DXPL to query
H5D_dxpl_cache_t *cache;IN/OUT: DXPL cache to fill with values
RETURNS
Non-negative on success/Negative on failure.
DESCRIPTION
Query all the values from a DXPL that are needed by internal routines
within the library.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The CACHE pointer should point at already allocated memory to place
non-default property list info. If a default property list is used, the
CACHE pointer will be changed to point at the default information.
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
herr_t
H5D__get_dxpl_cache(hid_t dxpl_id, H5D_dxpl_cache_t **cache)
{
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Check args */
HDassert(cache);
/* Check for the default DXPL */
if(dxpl_id==H5P_DATASET_XFER_DEFAULT)
*cache=&H5D_def_dxpl_cache;
else
if(H5D__get_dxpl_cache_real(dxpl_id,*cache) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't retrieve DXPL values")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D__get_dxpl_cache() */
/*-------------------------------------------------------------------------
* 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_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);
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;
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, 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)
{
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 */
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
HDassert(dset);
/* 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, dxpl_id, &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 {
/* 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)
{
H5D_shared_t *new_dset = NULL; /* New dataset object */
H5P_genplist_t *plist; /* Property list created */
H5D_shared_t *ret_value; /* 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
*
* 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_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?")
/* 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, 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__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_STATIC
/* Sanity checking */
HDassert(file);
HDassert(dset);
HDassert(space);
/* Get the file's 'use the latest version of the format' flag */
use_latest_format = H5F_USE_LATEST_FORMAT(file);
/* Copy dataspace for dataset */
if(NULL == (dset->shared->space = H5S_copy(space, FALSE, TRUE)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dataspace")
/* Set the latest format, if requested */
if(use_latest_format)
if(H5S_set_latest_version(dset->shared->space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype")
/* Set the dataset's dataspace to 'all' selection */
if(H5S_select_all(dset->shared->space, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set all selection")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__init_space() */
/*-------------------------------------------------------------------------
* Function: H5D__update_oh_info
*
* Purpose: Create and fill object header for dataset
*
* Return: Success: SUCCEED
* Failure: FAIL
*
* Programmer: Bill Wendling
* Thursday, October 31, 2002
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, 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 */
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 */
hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */
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;
/* 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, 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, 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->storage.u.compact.size;
/* Create an object header for the dataset */
if(H5O_create(file, dxpl_id, 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, dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header")
/* Write the dataspace 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")
/* Write the datatype header message */
if(H5O_msg_append_oh(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")
/* Write new fill value message */
if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0)
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_oh(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/create the layout (and I/O pipeline & EFL) messages */
if(H5D__layout_oh_create(file, dxpl_id, oh, dset, dapl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout/pline/efl header message")
/* 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) {
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 using older format. */
/* (If using the latest format, the modification time is part of the object
* header and doesn't use a separate message -QAK)
*/
if(!use_latest_format)
if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message")
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(dset->shared->layout.type == H5D_CHUNKED && layout_init) {
if(H5D__chunk_dest(file, dxpl_id, dset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache")
} /* end if */
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__update_oh_info() */
/*-------------------------------------------------------------------------
* 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 dapl_id, hid_t dxpl_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 */
H5G_loc_t dset_loc; /* Dataset location */
H5D_t *ret_value; /* 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));
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, 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 */
/* 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_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter")
layout = &new_dset->shared->layout;
if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, layout) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout")
if(pline->nused > 0 && H5D_CHUNKED != layout->type)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout")
fill = &new_dset->shared->dcpl_cache.fill;
if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill) < 0)
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->type == H5D_COMPACT && fill->alloc_time != H5D_ALLOC_TIME_EARLY)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset must have early space allocation")
/* If MPI VFD is used, no filter support yet. */
if(H5F_HAS_FEATURE(file, H5FD_FEAT_HAS_MPI) && pline->nused > 0)
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet")
/* 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 layout, pline & fill messages, if requested */
if(H5F_USE_LATEST_FORMAT(file)) {
/* Set the latest version for the I/O pipeline message */
if(H5O_pline_set_latest_version(&new_dset->shared->dcpl_cache.pline) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of I/O filter pipeline")
/* Set the latest version for the fill value message */
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(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)(file, new_dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to construct layout information")
/* Update the dataset's object header info. */
if(H5D__update_oh_info(file, dxpl_id, new_dset, dapl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache")
/* Indicate that the layout information was initialized */
layout_init = TRUE;
/* Add the dataset to the list of opened objects in the file */
if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count")
if(H5FO_insert(new_dset->oloc.file, new_dset->oloc.addr, new_dset->shared, TRUE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects")
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 && layout_init) {
if(H5D__chunk_dest(file, dxpl_id, new_dset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy chunk cache")
} /* end if */
if(new_dset->shared->space && 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), dxpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement refcount on newly created object")
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 && 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 = 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
*
* 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 dapl_id, hid_t dxpl_id)
{
H5D_shared_t *shared_fo = NULL;
H5D_t *dataset = NULL;
H5D_t *ret_value; /* 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")
/* 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, 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 */
/* Set the dataset to return */
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 */
dataset->shared = H5FL_FREE(H5D_shared_t, dataset->shared);
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__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 dapl_id, hid_t dxpl_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(dxpl_id, dataset->oloc.addr, FAIL)
/* 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(H5T_set_loc(dataset->shared->type, dataset->oloc.file, H5T_LOC_DISK) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid datatype location")
if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc), dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header")
/* Get a datatype ID for the dataset's datatype */
if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type, 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, dxpl_id, 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;
/* 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, dxpl_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, dxpl_id))
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, dxpl_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, dxpl_id))
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_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))
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)) {
if(H5D__alloc_storage(dataset, dxpl_id, 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)) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header")
if(dataset->shared) {
if(dataset->shared->layout.type == H5D_CHUNKED && layout_init)
if(H5D__chunk_dest(dataset->oloc.file, dxpl_id, dataset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache")
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(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, FAIL)
} /* 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(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, H5AC_dxpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to flush cached dataset info")
/* 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 */
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:
/* 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 */
/* Flush and destroy chunks in the cache. Continue to close even if
* it fails. */
if(H5D__chunk_dest(dataset->oloc.file, H5AC_dxpl_id, dataset) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache")
break;
case H5D_COMPACT:
/* Free the buffer for the raw data for compact datasets */
dataset->shared->layout.storage.u.compact.buf = H5MM_xfree(dataset->shared->layout.storage.u.compact.buf);
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 */
/*
* 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 = (unsigned)(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;
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)) < 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_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_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
*
* Programmer: Quincey Koziol
* Monday, September 12, 2005
*
*-------------------------------------------------------------------------
*/
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
*
* Programmer: Robb Matzke
* Thursday, June 4, 1998
*
*-------------------------------------------------------------------------
*/
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
*
* Programmer: Robb Matzke
* Friday, January 16, 1998
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc,
hbool_t full_overwrite, hsize_t old_dim[])
{
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, dxpl_id, &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 B-tree that describes chunked storage */
if(H5D__chunk_create(dset /*in,out*/, dxpl_id) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage")
/* Indicate that we set the storage addr */
addr_set = TRUE;
/* Indicate that we should initialize storage space */
must_init_space = TRUE;
} /* end if */
/* If space allocation is set to 'early' and we are extending
* the dataset, indicate that space should be allocated, so the
* B-tree gets expanded. -QAK
*/
if(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY
&& time_alloc == H5D_ALLOC_EXTEND)
must_init_space = TRUE;
break;
case H5D_COMPACT:
/* Check if space is already allocated */
if(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_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 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, old_dim, 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, old_dim, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value")
} /* end if */
} /* 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, dxpl_id, 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
*
* Programmer: Robb Matzke
* Monday, October 5, 1998
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__init_storage(const H5D_t *dset, hbool_t full_overwrite, hsize_t old_dim[],
hid_t dxpl_id)
{
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, 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.
*/
{
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(dset, dxpl_id, full_overwrite, old_dim) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset")
break;
} /* end block */
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
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__get_storage_size(H5D_t *dset, hid_t dxpl_id, hsize_t *storage_size)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE_TAG(dxpl_id, dset->oloc.addr, FAIL)
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, dxpl_id, 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_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, 0)
} /* 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 ret_value = HADDR_UNDEF;
FUNC_ENTER_PACKAGE
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. */
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__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_PACKAGE_NOERR
/* 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(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_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
*
* 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_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->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_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
*
* 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_PACKAGE_TAG(dxpl_id, dset->oloc.addr, FAIL)
/* 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")
/* Get the data space */
space = dset->shared->space;
/* Check if we are shrinking or expanding any of the dimensions */
if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions")
/* Modify the size of the data space */
if((changed = H5S_set_extent(space, size)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space")
/* Don't bother updating things, unless they've changed */
if(changed) {
hbool_t shrink = FALSE; /* Flag to indicate a dimension has shrank */
hbool_t expand = FALSE; /* Flag to indicate a dimension has grown */
unsigned u; /* Local index variable */
/* Determine if we are shrinking and/or expanding any dimensions */
for(u = 0; u < (unsigned)rank; u++) {
if(size[u] < curr_dims[u])
shrink = TRUE;
if(size[u] > curr_dims[u])
expand = TRUE;
} /* end for */
/*-------------------------------------------------------------------------
* Modify the dataset storage
*-------------------------------------------------------------------------
*/
/* Update the index values for the cached chunks for this dataset */
if(H5D_CHUNKED == dset->shared->layout.type) {
/* Update the cached chunk info */
if(H5D__chunk_set_info(dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to update # of chunks")
if(H5D__chunk_update_cache(dset, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices")
} /* end if */
/* Allocate space for the new parts of the dataset, if appropriate */
if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY)
if(H5D__alloc_storage(dset, dxpl_id, H5D_ALLOC_EXTEND, FALSE, curr_dims) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to extend dataset storage")
/*-------------------------------------------------------------------------
* Remove chunk information in the case of chunked datasets
* This removal takes place only in case we are shrinking the dateset
* and if the chunks are written
*-------------------------------------------------------------------------
*/
if(shrink && H5D_CHUNKED == dset->shared->layout.type &&
(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage))
/* Remove excess chunks */
if(H5D__chunk_prune_by_extent(dset, dxpl_id, curr_dims) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks")
/* Mark the dataspace as dirty, for later writing to the file */
if(H5D__mark(dset, dxpl_id, 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, FAIL)
} /* 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
*
* Programmer: Quincey Koziol
* July 27, 2009
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__flush_sieve_buf(H5D_t *dataset, hid_t dxpl_id)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_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, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed")
/* Reset sieve buffer dirty flag */
dataset->shared->cache.contig.sieve_dirty = FALSE;
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__flush_sieve_buf() */
/*-------------------------------------------------------------------------
* Function: H5D__flush_real
*
* Purpose: Flush any dataset information cached in memory
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* December 6, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__flush_real(H5D_t *dataset, hid_t dxpl_id)
{
H5O_t *oh = NULL; /* Pointer to dataset's object header */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE_TAG(dxpl_id, dataset->oloc.addr, FAIL)
/* Check args */
HDassert(dataset);
/* Check for metadata changes that will require updating the object's modification time */
if(dataset->shared->layout_dirty || dataset->shared->space_dirty) {
unsigned update_flags = H5O_UPDATE_TIME; /* Modification time flag */
/* Pin the object header */
if(NULL == (oh = H5O_pin(&dataset->oloc, dxpl_id)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header")
/* Update the layout on disk, if it's been changed */
if(dataset->shared->layout_dirty) {
if(H5D__layout_oh_write(dataset, dxpl_id, oh, update_flags) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout/pline/efl info")
dataset->shared->layout_dirty = FALSE;
/* Reset the "update the modification time" flag, so we only do it once */
update_flags = 0;
} /* end if */
/* Update the dataspace on disk, if it's been changed */
if(dataset->shared->space_dirty) {
if(H5S_write(dataset->oloc.file, dxpl_id, oh, update_flags, dataset->shared->space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace")
dataset->shared->space_dirty = FALSE;
/* 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 */
/* Flush cached raw data for each kind of dataset layout */
if(dataset->shared->layout.ops->flush &&
(dataset->shared->layout.ops->flush)(dataset, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush raw data")
done:
/* Release pointer to object header */
if(oh != NULL)
if(H5O_unpin(oh) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header")
FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL)
} /* end H5D__flush_real() */
/*-------------------------------------------------------------------------
* Function: H5D__mark
*
* Purpose: Mark some aspect of a dataset as dirty
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* July 4, 2008
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__mark(const H5D_t *dataset, hid_t UNUSED dxpl_id, unsigned flags)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE_NOERR
/* Check args */
HDassert(dataset);
HDassert(!(flags & (unsigned)~(H5D_MARK_SPACE | H5D_MARK_LAYOUT)));
/* Mark aspects of the dataset as dirty */
if(flags & H5D_MARK_SPACE)
dataset->shared->space_dirty = TRUE;
if(flags & H5D_MARK_LAYOUT)
dataset->shared->layout_dirty = TRUE;
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mark() */
/*-------------------------------------------------------------------------
* Function: H5D__flush_cb
*
* Purpose: Flush any dataset information cached in memory
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Quincey Koziol
* November 8, 2007
*
*-------------------------------------------------------------------------
*/
static int
H5D__flush_cb(void *_dataset, hid_t UNUSED id, void *_udata)
{
H5D_t *dataset = (H5D_t *)_dataset; /* Dataset pointer */
H5D_flush_ud_t *udata = (H5D_flush_ud_t *)_udata; /* User data for callback */
int ret_value = H5_ITER_CONT; /* Return value */
FUNC_ENTER_STATIC
/* Check args */
HDassert(dataset);
/* Check for dataset in same file */
if(udata->f == dataset->oloc.file) {
/* Flush the dataset's information */
if(H5D__flush_real(dataset, udata->dxpl_id) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, H5_ITER_ERROR, "unable to flush cached dataset info")
} /* end if */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__flush_cb() */
/*-------------------------------------------------------------------------
* Function: H5D_flush
*
* Purpose: Flush any dataset information cached in memory
*
* Return: Success: Non-negative
* Failure: Negative
*
* Programmer: Ray Lu
* August 14, 2002
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_flush(const H5F_t *f, hid_t dxpl_id)
{
H5D_flush_ud_t udata; /* User data for callback */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
/* Check args */
HDassert(f);
/* Set user data for callback */
udata.f = f;
udata.dxpl_id = dxpl_id;
/* Iterate over all the open datasets */
if(H5I_iterate(H5I_DATASET, H5D__flush_cb, &udata, FALSE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to flush cached dataset info")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_flush() */
/*-------------------------------------------------------------------------
* 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
*
* Programmer: Robb Matzke
* Tuesday, February 3, 1998
*
*-------------------------------------------------------------------------
*/
hid_t
H5D_get_create_plist(H5D_t *dset)
{
H5P_genplist_t *dcpl_plist; /* Dataset's DCPL */
H5P_genplist_t *new_plist; /* Copy of dataset's DCPL */
H5O_fill_t copied_fill; /* Fill value to tweak */
hid_t new_dcpl_id = FAIL;
hid_t ret_value; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
/* Check args */
if(NULL == (dcpl_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id)))
HGOTO_ERROR(H5E_ARGS, 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_ARGS, H5E_BADTYPE, FAIL, "can't get property list")
/* Retrieve any object creation properties */
if(H5O_get_create_plist(&dset->oloc, H5AC_ind_dxpl_id, new_plist) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get object creation info")
/* Get the fill value property */
if(H5P_get(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0)
HGOTO_ERROR(H5E_PLIST, 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, NULL, NULL, H5AC_ind_dxpl_id, FALSE)))
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_DATATYPE, 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_RESOURCE, H5E_NOSPACE, 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, H5AC_ind_dxpl_id) < 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 fill value property to property list */
if(H5P_set(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property list fill value")
/* 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
*
* Programmer: Mohamad Chaarawi
* March, 2012
*
*-------------------------------------------------------------------------
*/
hid_t
H5D_get_access_plist(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 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")
} /* end if */
/* 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")
} /* end if */
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
*
* Programmer: Mohamad Chaarawi
* March, 2012
*
*-------------------------------------------------------------------------
*/
hid_t
H5D_get_space(H5D_t *dset)
{
H5S_t *space = NULL;
hid_t ret_value = FAIL;
FUNC_ENTER_NOAPI_NOINIT
/* Read the data space message and return a data space object */
if(NULL == (space = H5S_copy(dset->shared->space, FALSE, TRUE)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get data space")
/* 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
*
* Programmer: Mohamad Chaarawi
* March, 2012
*
*-------------------------------------------------------------------------
*/
hid_t
H5D_get_type(H5D_t *dset)
{
H5T_t *dt = NULL;
hid_t ret_value = FAIL;
FUNC_ENTER_NOAPI_NOINIT
/* 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")
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D_get_type() */
Reference in New Issue View Git Blame Copy Permalink