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Diffstat (limited to 'src/H5Dint.c')
| -rw-r--r-- | src/H5Dint.c | 3676 |
1 files changed, 3676 insertions, 0 deletions
diff --git a/src/H5Dint.c b/src/H5Dint.c new file mode 100644 index 0000000..1813ca6 --- /dev/null +++ b/src/H5Dint.c @@ -0,0 +1,3676 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/****************/ +/* Module Setup */ +/****************/ + +#include "H5Dmodule.h" /* This source code file is part of the H5D module */ + + +/***********/ +/* Headers */ +/***********/ +#include "H5private.h" /* Generic Functions */ +#include "H5Dpkg.h" /* Datasets */ +#include "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__cache_dataspace_info(const H5D_t *dset); +static herr_t H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space); +static herr_t H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, + hid_t dapl_id); +static herr_t H5D_build_extfile_prefix(const H5D_t *dset, hid_t dapl_id, + char **extfile_prefix); +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_io_info_t *io_info, hbool_t full_overwrite, + hsize_t old_dim[]); +static herr_t H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id); + +/*********************/ +/* 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 */ +}}; + +/* Flag indicating "top" of interface has been initialized */ +static hbool_t H5D_top_package_initialize_s = FALSE; + + + +/*------------------------------------------------------------------------- + * Function: H5D_init + * + * Purpose: Initialize the interface from some other layer. + * + * Return: Success: non-negative + * + * Failure: negative + * + * 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_package -- Initialize interface-specific information +USAGE + herr_t H5D__init_package() + +RETURNS + Non-negative on success/Negative on failure +DESCRIPTION + Initializes any interface-specific data or routines. +NOTES + Care must be taken when using the H5P functions, since they can cause + a deadlock in the library when the library is attempting to terminate -QAK + +--------------------------------------------------------------------------*/ +herr_t +H5D__init_package(void) +{ + H5P_genplist_t *def_dcpl; /* Default Dataset Creation Property list */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Initialize the atom group for the dataset IDs */ + if(H5I_register_type(H5I_DATASET_CLS) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize interface") + + /* Reset the "default dataset" information */ + HDmemset(&H5D_def_dset, 0, sizeof(H5D_shared_t)); + + /* Get the default dataset creation property list values and initialize the + * default dataset with them. + */ + if(NULL == (def_dcpl = (H5P_genplist_t *)H5I_object(H5P_LST_DATASET_CREATE_ID_g))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get default dataset creation property list") + + /* Get the default data storage layout */ + if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve layout") + + /* Get the default dataset creation properties */ + if(H5P_get(def_dcpl, H5D_CRT_EXT_FILE_LIST_NAME, &H5D_def_dset.dcpl_cache.efl) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve external file list") + if(H5P_get(def_dcpl, H5D_CRT_FILL_VALUE_NAME, &H5D_def_dset.dcpl_cache.fill) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value") + if(H5P_get(def_dcpl, H5O_CRT_PIPELINE_NAME, &H5D_def_dset.dcpl_cache.pline) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve pipeline filter") + + /* 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") + + /* Mark "top" of interface as initialized, too */ + H5D_top_package_initialize_s = TRUE; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__init_package() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_top_term_package + * + * Purpose: Close the "top" of the interface, releasing IDs, etc. + * + * Return: Success: Positive if anything was done that might + * affect other interfaces; zero otherwise. + * Failure: Negative. + * + * Programmer: Quincey Koziol + * Sunday, September 13, 2015 + * + *------------------------------------------------------------------------- + */ +int +H5D_top_term_package(void) +{ + int n = 0; + + FUNC_ENTER_NOAPI_NOINIT_NOERR + + if(H5D_top_package_initialize_s) { + if(H5I_nmembers(H5I_DATASET) > 0) { + /* The dataset API uses the "force" flag set to true because it + * is using the "file objects" (H5FO) API functions to track open + * objects in the file. Using the H5FO code means that dataset + * IDs can have reference counts >1, when an existing dataset is + * opened more than once. However, the H5I code does not attempt + * to close objects with reference counts>1 unless the "force" flag + * is set to true. + * + * At some point (probably after the group and datatypes use the + * the H5FO code), the H5FO code might need to be switched around + * to storing pointers to the objects being tracked (H5D_t, H5G_t, + * etc) and reference count those itself instead of relying on the + * reference counting in the H5I layer. Then, the "force" flag can + * be put back to false. + * + * Setting the "force" flag to true for all the interfaces won't + * work because the "file driver" (H5FD) APIs use the H5I reference + * counting to avoid closing a file driver out from underneath an + * open file... + * + * QAK - 5/13/03 + */ + (void)H5I_clear_type(H5I_DATASET, TRUE, FALSE); + n++; /*H5I*/ + } /* end if */ + + /* Mark closed */ + if(0 == n) + H5D_top_package_initialize_s = FALSE; + } /* end if */ + + FUNC_LEAVE_NOAPI(n) +} /* end H5D_top_term_package() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_term_package + * + * Purpose: Terminate this interface. + * + * Note: Finishes shutting down the interface, after + * H5D_top_term_package() is called + * + * Return: Success: Positive if anything was done that might + * affect other interfaces; zero otherwise. + * Failure: Negative. + * + * Programmer: Robb Matzke + * Friday, November 20, 1998 + * + *------------------------------------------------------------------------- + */ +int +H5D_term_package(void) +{ + int n = 0; + + FUNC_ENTER_NOAPI_NOINIT_NOERR + + if(H5_PKG_INIT_VAR) { + /* Sanity checks */ + HDassert(0 == H5I_nmembers(H5I_DATASET)); + HDassert(FALSE == H5D_top_package_initialize_s); + + /* Destroy the dataset object id group */ + n += (H5I_dec_type_ref(H5I_DATASET) > 0); + + /* Mark closed */ + if(0 == n) + H5_PKG_INIT_VAR = FALSE; + } /* end if */ + + FUNC_LEAVE_NOAPI(n) +} /* end H5D_term_package() */ + + +/*-------------------------------------------------------------------------- + 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") + + /* Look at the data transform property */ + /* (Note: 'peek', not 'get' - if this turns out to be a problem, we should + * add a H5D__free_dxpl_cache() routine. -QAK) + */ + if(H5P_peek(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 = NULL; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check arguments */ + HDassert(loc); + HDassert(name && *name); + HDassert(type_id != H5P_DEFAULT); + HDassert(space); + HDassert(lcpl_id != H5P_DEFAULT); + HDassert(dcpl_id != H5P_DEFAULT); + HDassert(dapl_id != H5P_DEFAULT); + 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); + + /* Check for chunked layout */ + if(dset->shared->layout.type == H5D_CHUNKED) { + /* For chunked layout set the space status by the storage size */ + /* Get the dataset's dataspace */ + HDassert(dset->shared->space); + + /* Get the total number of elements in dataset's dataspace */ + if((snelmts = H5S_GET_EXTENT_NPOINTS(dset->shared->space)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace") + nelmts = (hsize_t)snelmts; + + /* Get the size of the dataset's datatype */ + if(0 == (dt_size = H5T_GET_SIZE(dset->shared->type))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype") + + /* Compute the maximum size of the dataset in bytes */ + full_size = nelmts * dt_size; + + /* Check for overflow during multiplication */ + if(nelmts != (full_size / dt_size)) + HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed") + + /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */ + if(H5D__get_storage_size(dset, 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 + *allocation = H5D_SPACE_STATUS_PART_ALLOCATED; + } /* end if */ + else { + /* For non-chunked layouts set space status by result of is_space_alloc + * function */ + if(dset->shared->layout.ops->is_space_alloc(&dset->shared->layout.storage)) + *allocation = H5D_SPACE_STATUS_ALLOCATED; + else + *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED; + } /* end else */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__get_space_status() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__new + * + * Purpose: Creates a new, empty dataset structure + * + * Return: Success: Pointer to a new dataset descriptor. + * + * Failure: NULL + * + * 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 = NULL; /* Return value */ + + FUNC_ENTER_STATIC + + /* Allocate new shared dataset structure */ + if(NULL == (new_dset = H5FL_MALLOC(H5D_shared_t))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + + /* Copy the default dataset information */ + HDmemcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t)); + + /* If we are using the default dataset creation property list, during creation + * don't bother to copy it, just increment the reference count + */ + if(!vl_type && creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) { + if(H5I_inc_ref(dcpl_id, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment default DCPL ID") + new_dset->dcpl_id = dcpl_id; + } /* end if */ + else { + /* Get the property list */ + if(NULL == (plist = (H5P_genplist_t *)H5I_object(dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list") + + new_dset->dcpl_id = H5P_copy_plist(plist, FALSE); + } /* end else */ + + /* Set return value */ + ret_value = new_dset; + +done: + if(ret_value == NULL) + if(new_dset != NULL) { + if(new_dset->dcpl_id != 0 && H5I_dec_ref(new_dset->dcpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "can't decrement temporary datatype ID") + new_dset = H5FL_FREE(H5D_shared_t, new_dset); + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__new() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__init_type + * + * Purpose: Copy a datatype for a dataset's use, performing all the + * necessary adjustments, etc. + * + * Return: Success: SUCCEED + * Failure: FAIL + * + * 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 'latest datatype version support' is enabled */ + 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 datatype version support' flag */ + use_latest_format = H5F_USE_LATEST_FLAGS(file, H5F_LATEST_DATATYPE); + + /* 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") + + /* Convert a datatype (if committed) to a transient type if the committed datatype's file + location is different from the file location where the dataset will be created */ + if(H5T_convert_committed_datatype(dset->shared->type, file) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't get shared datatype info") + + /* Mark any datatypes as being on disk now */ + if(H5T_set_loc(dset->shared->type, file, H5T_LOC_DISK) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't set datatype location") + + /* Set the 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__cache_dataspace_info + * + * Purpose: Cache dataspace info for a dataset + * + * Return: Success: SUCCEED + * Failure: FAIL + * + * Programmer: Quincey Koziol + * Wednesday, November 19, 2014 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__cache_dataspace_info(const H5D_t *dset) +{ + int sndims; /* Signed number of dimensions of dataspace rank */ + unsigned u; /* Local index value */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity checking */ + HDassert(dset); + + /* Cache info for dataset's dataspace */ + if((sndims = H5S_get_simple_extent_dims(dset->shared->space, dset->shared->curr_dims, dset->shared->max_dims)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't cache dataspace dimensions") + dset->shared->ndims = (unsigned)sndims; + + /* Compute the inital 'power2up' values */ + for(u = 0; u < dset->shared->ndims; u++) + dset->shared->curr_power2up[u] = H5VM_power2up(dset->shared->curr_dims[u]); + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__cache_dataspace_info() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__init_space + * + * Purpose: Copy a dataspace for a dataset's use, performing all the + * necessary adjustments, etc. + * + * Return: Success: SUCCEED + * Failure: FAIL + * + * 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 'latest dataspace version support' is enabled */ + 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 dataspace version support' flag */ + use_latest_format = H5F_USE_LATEST_FLAGS(file, H5F_LATEST_DATASPACE); + + /* Copy dataspace for dataset */ + if(NULL == (dset->shared->space = H5S_copy(space, FALSE, TRUE))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dataspace") + + /* Cache the dataset's dataspace info */ + if(H5D__cache_dataspace_info(dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't cache dataspace info") + + /* Set the 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 */ + 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; + + /* 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 fill message version support') */ + if(fill_prop->buf && !(H5F_USE_LATEST_FLAGS(file, H5F_LATEST_FILL_MSG))) { + 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) && + (H5P_exist_plist(dc_plist, H5O_BOGUS_MSG_ID_NAME) > 0) ) { + + uint8_t bogus_flags = 0; /* Flags for creating "bogus" message */ + unsigned bogus_id; /* "bogus" ID */ + + /* Retrieve "bogus" message ID */ + if(H5P_get(dc_plist, H5O_BOGUS_MSG_ID_NAME, &bogus_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get bogus ID options") + /* Retrieve "bogus" message flags */ + if(H5P_get(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME, &bogus_flags) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get bogus message options") + + /* Add a "bogus" message (for error testing). */ + if(H5O_bogus_oh(file, dxpl_id, oh, bogus_id, (unsigned)bogus_flags) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create 'bogus' message") + } /* end if */ +} +#endif /* H5O_ENABLE_BOGUS */ + + /* Add a modification time message, if using older format. */ + /* (If using the latest 'no modification time message' version support, the modification time is part of the object + * header and doesn't use a separate message -QAK) + */ + if(!(H5F_USE_LATEST_FLAGS(file, H5F_LATEST_NO_MOD_TIME_MSG))) + 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(layout_init) + /* Destroy the layout information for the dataset */ + if(dset->shared->layout.ops->dest && (dset->shared->layout.ops->dest)(dset, dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__update_oh_info() */ + + +/*-------------------------------------------------------------------------- + * Function: H5D_build_extfile_prefix + * + * Purpose: Determine the external file prefix to be used and store + * it in extfile_prefix. Stores an empty string if no prefix + * should be used. + * + * Return: SUCCEED/FAIL + * + * Programmer: Steffen Kiess + * October 16, 2015 + *-------------------------------------------------------------------------- + */ +static herr_t +H5D_build_extfile_prefix(const H5D_t *dset, hid_t dapl_id, char **extfile_prefix /*out*/) +{ + char *prefix = NULL; /* prefix used to look for the file */ + char *extpath = NULL; /* absolute path of directory the HDF5 file is in */ + size_t extpath_len; /* length of extpath */ + size_t prefix_len; /* length of prefix */ + size_t extfile_prefix_len; /* length of expanded prefix */ + H5P_genplist_t *plist = NULL; /* Property list pointer */ + herr_t ret_value = SUCCEED; /* Return value */ + + + FUNC_ENTER_NOAPI_NOINIT + + HDassert(dset); + HDassert(dset->oloc.file); + + extpath = H5F_EXTPATH(dset->oloc.file); + HDassert(extpath); + + /* XXX: Future thread-safety note - getenv is not required + * to be reentrant. + */ + prefix = HDgetenv("HDF5_EXTFILE_PREFIX"); + + if(prefix == NULL || *prefix == '\0') { + /* Set prefix to value of H5D_ACS_EFILE_PREFIX_NAME property */ + if(NULL == (plist = H5P_object_verify(dapl_id, H5P_DATASET_ACCESS))) + HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID") + if(H5P_peek(plist, H5D_ACS_EFILE_PREFIX_NAME, &prefix) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file prefix") + } /* end if */ + + /* Prefix has to be checked for NULL / empty string again because the + * code above might have updated it. + */ + if(prefix == NULL || *prefix == '\0' || HDstrcmp(prefix, ".") == 0) { + /* filename is interpreted as relative to the current directory, + * does not need to be expanded + */ + if(NULL == (*extfile_prefix = (char *)H5MM_strdup(""))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") + } /* end if */ + else { + if (HDstrncmp(prefix, "${ORIGIN}", HDstrlen("${ORIGIN}")) == 0) { + /* Replace ${ORIGIN} at beginning of prefix by directory of HDF5 file */ + extpath_len = HDstrlen(extpath); + prefix_len = HDstrlen(prefix); + extfile_prefix_len = extpath_len + prefix_len - HDstrlen("${ORIGIN}") + 1; + + if(NULL == (*extfile_prefix = (char *)H5MM_malloc(extfile_prefix_len))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate buffer") + HDsnprintf(*extfile_prefix, extfile_prefix_len, "%s%s", extpath, prefix + HDstrlen("${ORIGIN}")); + } /* end if */ + else { + if(NULL == (*extfile_prefix = (char *)H5MM_strdup(prefix))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") + } /* end else */ + } /* end else */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D_build_extfile_prefix() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__create + * + * Purpose: Creates a new dataset with name NAME in file F and associates + * with it a datatype TYPE for each element as stored in the + * file, dimensionality information or dataspace SPACE, and + * other miscellaneous properties CREATE_PARMS. All arguments + * are deep-copied before being associated with the new dataset, + * so the caller is free to subsequently modify them without + * affecting the dataset. + * + * Return: Success: Pointer to a new dataset + * + * Failure: NULL + * + * 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 */ + hbool_t layout_copied = FALSE; /* Flag to indicate that layout message was copied */ + hbool_t fill_copied = FALSE; /* Flag to indicate that fill-value message was copied */ + hbool_t pline_copied = FALSE; /* Flag to indicate that pipeline message was copied */ + hbool_t efl_copied = FALSE; /* Flag to indicate that external file list message was copied */ + H5G_loc_t dset_loc; /* Dataset location */ + H5D_t *ret_value = NULL; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* check args */ + HDassert(file); + HDassert(H5I_DATATYPE == H5I_get_type(type_id)); + HDassert(space); + HDassert(H5I_GENPROP_LST == H5I_get_type(dcpl_id)); + 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 */ + H5O_efl_t *efl; /* Dataset's external file list info */ + + /* Check if the filters in the DCPL can be applied to this dataset */ + if(H5Z_can_apply(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_CANTINIT, NULL, "I/O filters can't operate on this dataset") + + /* Make the "set local" filter callbacks for this dataset */ + if(H5Z_set_local(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set local filter parameters") + + /* Get new dataset's property list object */ + if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(new_dset->shared->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list") + + /* Retrieve the properties we need */ + pline = &new_dset->shared->dcpl_cache.pline; + if(H5P_get(dc_plist, H5O_CRT_PIPELINE_NAME, pline) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't retrieve pipeline filter") + pline_copied = TRUE; + layout = &new_dset->shared->layout; + if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, layout) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't retrieve layout") + layout_copied = TRUE; + fill = &new_dset->shared->dcpl_cache.fill; + if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't retrieve fill value info") + fill_copied = TRUE; + efl = &new_dset->shared->dcpl_cache.efl; + if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't retrieve external file list") + efl_copied = TRUE; + + /* Check that chunked layout is used if filters are enabled */ + if(pline->nused > 0 && H5D_CHUNKED != layout->type) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout") + + /* Check if the alloc_time is the default and error out */ + if(fill->alloc_time == H5D_ALLOC_TIME_DEFAULT) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "invalid space allocation state") + + /* Don't allow compact datasets to allocate space later */ + if(layout->type == H5D_COMPACT && fill->alloc_time != H5D_ALLOC_TIME_EARLY) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset must have early space allocation") + + /* 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") + } /* end if */ + + /* Set the latest version of the layout, pline & fill messages, if requested */ + if(H5F_USE_LATEST_FLAGS(file, H5F_LATEST_DSET_MSG_FLAGS)) { + /* Set the latest version for the I/O pipeline message */ + if(H5F_USE_LATEST_FLAGS(file, H5F_LATEST_PLINE_MSG)) + 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 message */ + if(H5F_USE_LATEST_FLAGS(file, H5F_LATEST_FILL_MSG)) + /* 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") + + /* Set the latest version for the layout message */ + if(H5F_USE_LATEST_FLAGS(file, H5F_LATEST_LAYOUT_MSG)) + /* Set the latest version for the layout message */ + if(H5D__layout_set_latest_version(&new_dset->shared->layout, new_dset->shared->space, &new_dset->shared->dcpl_cache) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of layout") + } /* end if */ + else if(new_dset->shared->layout.version >= H5O_LAYOUT_VERSION_4) { + /* Use latest indexing type for layout message version >= 4 */ + if(H5D__layout_set_latest_indexing(&new_dset->shared->layout, new_dset->shared->space, &new_dset->shared->dcpl_cache) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest indexing") + } /* end if */ + + /* Check if this dataset is going into a parallel file and set space allocation time */ + if(H5F_HAS_FEATURE(file, H5FD_FEAT_ALLOCATE_EARLY)) + new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY; + + /* Set the dataset's I/O operations */ + if(H5D__layout_set_io_ops(new_dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize I/O operations") + + /* Create the layout information for the new dataset */ + if(new_dset->shared->layout.ops->construct && (new_dset->shared->layout.ops->construct)(file, new_dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to construct layout information") + + /* Update the dataset's object header info. */ + if(H5D__update_oh_info(file, 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; + + /* Set up append flush parameters for the dataset */ + if(H5D__append_flush_setup(new_dset, dapl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set up flush append property") + + /* Set the external file prefix */ + if(H5D_build_extfile_prefix(new_dset, dapl_id, &new_dset->shared->extfile_prefix) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix") + + /* Add the dataset to the list of opened objects in the file */ + if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count") + if(H5FO_insert(new_dset->oloc.file, new_dset->oloc.addr, new_dset->shared, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects") + new_dset->shared->fo_count = 1; + + /* Success */ + ret_value = new_dset; + +done: + if(!ret_value && new_dset && new_dset->shared) { + if(new_dset->shared) { + if(layout_init) + if(new_dset->shared->layout.ops->dest && (new_dset->shared->layout.ops->dest)(new_dset, dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy layout info") + if(pline_copied) + if(H5O_msg_reset(H5O_PLINE_ID, &new_dset->shared->dcpl_cache.pline) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, NULL, "unable to reset I/O pipeline info") + if(layout_copied) + if(H5O_msg_reset(H5O_LAYOUT_ID, &new_dset->shared->layout) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, NULL, "unable to reset layout info") + if(fill_copied) + if(H5O_msg_reset(H5O_FILL_ID, &new_dset->shared->dcpl_cache.fill) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, NULL, "unable to reset fill-value info") + if(efl_copied) + if(H5O_msg_reset(H5O_EFL_ID, &new_dset->shared->dcpl_cache.efl) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, NULL, "unable to reset external file list info") + if(new_dset->shared->space && H5S_close(new_dset->shared->space) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace") + if(new_dset->shared->type && H5I_dec_ref(new_dset->shared->type_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype") + if(H5F_addr_defined(new_dset->oloc.addr)) { + if(H5O_dec_rc_by_loc(&(new_dset->oloc), dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement refcount on newly created object") + if(H5O_close(&(new_dset->oloc), NULL) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header") + if(file) { + if(H5O_delete(file, 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->extfile_prefix = (char *)H5MM_xfree(new_dset->shared->extfile_prefix); + new_dset->shared = H5FL_FREE(H5D_shared_t, new_dset->shared); + } /* end if */ + new_dset->oloc.file = NULL; + new_dset = H5FL_FREE(H5D_t, new_dset); + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__create() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__open_name + * + * Purpose: Opens an existing dataset by name. + * + * Return: Success: Ptr to a new dataset. + * Failure: NULL + * + * Programmer: Neil Fortner + * Friday, March 6, 2015 + * + *------------------------------------------------------------------------- + */ +H5D_t * +H5D__open_name(const H5G_loc_t *loc, const char *name, hid_t dapl_id, + hid_t dxpl_id) +{ + H5D_t *dset = NULL; + H5G_loc_t dset_loc; /* Object location of dataset */ + H5G_name_t path; /* Dataset group hier. path */ + H5O_loc_t oloc; /* Dataset object location */ + H5O_type_t obj_type; /* Type of object at location */ + hbool_t loc_found = FALSE; /* Location at 'name' found */ + H5D_t *ret_value = NULL; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check args */ + HDassert(loc); + HDassert(name); + + /* Set up dataset location to fill in */ + dset_loc.oloc = &oloc; + dset_loc.path = &path; + H5G_loc_reset(&dset_loc); + + /* Find the dataset object */ + if(H5G_loc_find(loc, name, &dset_loc, dapl_id, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found") + loc_found = TRUE; + + /* Check that the object found is the correct type */ + if(H5O_obj_type(&oloc, &obj_type, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't get object type") + if(obj_type != H5O_TYPE_DATASET) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, NULL, "not a dataset") + + /* Open the dataset */ + if(NULL == (dset = H5D_open(&dset_loc, dapl_id, dxpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't open dataset") + + /* Set return value */ + ret_value = dset; + +done: + if(!ret_value) + if(loc_found && H5G_loc_free(&dset_loc) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "can't free location") + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__open_name() */ + + +/* + *------------------------------------------------------------------------- + * Function: H5D_open + * + * Purpose: Checks if dataset is already open, or opens a dataset for + * access. + * + * Return: Success: Dataset ID + * Failure: FAIL + * + * 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; + char *extfile_prefix = NULL; /* Expanded external file prefix */ + H5D_t *ret_value = NULL; /* Return value */ + + FUNC_ENTER_NOAPI(NULL) + + /* check args */ + HDassert(loc); + + /* Allocate the dataset structure */ + if(NULL == (dataset = H5FL_CALLOC(H5D_t))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + + /* Shallow copy (take ownership) of the object location object */ + if(H5O_loc_copy(&(dataset->oloc), loc->oloc, H5_COPY_SHALLOW) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy object location") + + /* Shallow copy (take ownership) of the group hier. path */ + if(H5G_name_copy(&(dataset->path), loc->path, H5_COPY_SHALLOW) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy path") + + /* Get the external file prefix */ + if(H5D_build_extfile_prefix(dataset, dapl_id, &extfile_prefix) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix") + + /* Check if dataset was already open */ + if(NULL == (shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr))) { + /* Clear any errors from H5FO_opened() */ + H5E_clear_stack(NULL); + + /* Open the dataset object */ + if(H5D__open_oid(dataset, dapl_id, 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; + + /* Set the external file prefix */ + dataset->shared->extfile_prefix = extfile_prefix; + /* Prevent string from being freed during done: */ + extfile_prefix = NULL; + + } /* end if */ + else { + /* Point to shared info */ + dataset->shared = shared_fo; + + /* Increment # of datasets using shared information */ + shared_fo->fo_count++; + + /* Check whether the external file prefix of the already open dataset + * matches the new external file prefix + */ + if(HDstrcmp(extfile_prefix, dataset->shared->extfile_prefix) != 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "new external file prefix does not match external file prefix of already open dataset") + + /* Check if the object has been opened through the top file yet */ + if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) { + /* Open the object through this top file */ + if(H5O_open(&(dataset->oloc)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open object header") + } /* end if */ + + /* Increment object count for the object in the top file */ + if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count") + } /* end else */ + + /* Set the dataset to return */ + ret_value = dataset; + +done: + extfile_prefix = (char *)H5MM_xfree(extfile_prefix); + + if(ret_value == NULL) { + /* Free the location--casting away const*/ + if(dataset) { + if(shared_fo == NULL && dataset->shared) { /* Need to free shared fo */ + dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix); + dataset->shared = 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__flush_append_setup + * + * Purpose: Set the append flush parameters for a dataset + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi + * Wednesday, January 8, 2014 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id) +{ + herr_t ret_value = SUCCEED; /* return value */ + + FUNC_ENTER_STATIC + + /* Check args */ + HDassert(dset); + HDassert(dset->shared); + + /* Set default append flush values */ + HDmemset(&dset->shared->append_flush, 0, sizeof(dset->shared->append_flush)); + + /* If the dataset is chunked and there is a non-default DAPL */ + if(dapl_id != H5P_DATASET_ACCESS_DEFAULT && dset->shared->layout.type == H5D_CHUNKED) { + H5P_genplist_t *dapl; /* data access property list object pointer */ + + /* Get dataset access property list */ + if(NULL == (dapl = (H5P_genplist_t *)H5I_object(dapl_id))) + HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for dapl ID"); + + /* Check if append flush property exists */ + if(H5P_exist_plist(dapl, H5D_ACS_APPEND_FLUSH_NAME) > 0) { + H5D_append_flush_t info; + + /* Get append flush property */ + if(H5P_get(dapl, H5D_ACS_APPEND_FLUSH_NAME, &info) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get append flush info") + if(info.ndims > 0) { + hsize_t curr_dims[H5S_MAX_RANK]; /* current dimension sizes */ + hsize_t max_dims[H5S_MAX_RANK]; /* current dimension sizes */ + int rank; /* dataspace # of dimensions */ + unsigned u; /* local index variable */ + + /* Get dataset rank */ + if((rank = H5S_get_simple_extent_dims(dset->shared->space, curr_dims, max_dims)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") + if(info.ndims != (unsigned)rank) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "boundary dimension rank does not match dataset rank") + + /* Validate boundary sizes */ + for(u = 0; u < info.ndims; u++) + if(info.boundary[u] != 0) /* when a non-zero boundary is set */ + /* the dimension is extendible? */ + if(max_dims[u] != H5S_UNLIMITED && max_dims[u] == curr_dims[u]) + break; + + /* At least one boundary dimension is not extendible */ + if(u != info.ndims) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "boundary dimension is not valid") + + /* Copy append flush settings */ + dset->shared->append_flush.ndims = info.ndims; + dset->shared->append_flush.func = info.func; + dset->shared->append_flush.udata = info.udata; + HDmemcpy(dset->shared->append_flush.boundary, info.boundary, sizeof(info.boundary)); + } /* end if */ + } /* end if */ + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D__append_flush_setup() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__open_oid + * + * Purpose: Opens a dataset for access. + * + * Return: Dataset pointer on success, NULL on failure + * + * 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") + + /* Cache the dataset's dataspace info */ + if(H5D__cache_dataspace_info(dataset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't cache dataspace info") + + /* Get a datatype ID for the dataset's datatype */ + if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type, FALSE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") + + /* Get dataset creation property list object */ + if(NULL == (plist = (H5P_genplist_t *)H5I_object(dataset->shared->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") + + /* Get the layout/pline/efl message information */ + if(H5D__layout_oh_read(dataset, 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; + + /* Set up flush append property */ + if(H5D__append_flush_setup(dataset, dapl_id)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set up flush append property") + + /* Point at dataset's copy, to cache it for later */ + fill_prop = &dataset->shared->dcpl_cache.fill; + + /* Try to get the new fill value message from the object header */ + if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_FILL_NEW_ID, 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_VIRTUAL: + fill_prop->alloc_time = H5D_ALLOC_TIME_INCR; + break; + + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + default: + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet") + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + } /* end else */ + + /* If "old" fill value size is 0 (undefined), map it to -1 */ + if(fill_prop->size == 0) + fill_prop->size = (ssize_t)-1; + } /* end if */ + alloc_time_state = 0; + if((dataset->shared->layout.type == H5D_COMPACT && fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) + || (dataset->shared->layout.type == H5D_CONTIGUOUS && fill_prop->alloc_time == H5D_ALLOC_TIME_LATE) + || (dataset->shared->layout.type == H5D_CHUNKED && fill_prop->alloc_time == H5D_ALLOC_TIME_INCR) + || (dataset->shared->layout.type == H5D_VIRTUAL && fill_prop->alloc_time == H5D_ALLOC_TIME_INCR)) + alloc_time_state = 1; + + /* Set revised fill value properties, if they are different from the defaults */ + if(H5P_fill_value_cmp(&H5D_def_dset.dcpl_cache.fill, fill_prop, sizeof(H5O_fill_t))) { + if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set fill value") + if(H5P_set(plist, H5D_CRT_ALLOC_TIME_STATE_NAME, &alloc_time_state) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set allocation time state") + } /* end if */ + + /* + * Make sure all storage is properly initialized. + * This is important only for parallel I/O where the space must + * be fully allocated before I/O can happen. + */ + if((H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR) + && !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) + && H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_ALLOCATE_EARLY)) { + H5D_io_info_t io_info; + + io_info.dset = dataset; + io_info.raw_dxpl_id = H5AC_rawdata_dxpl_id; + io_info.md_dxpl_id = dxpl_id; + + if(H5D__alloc_storage(&io_info, H5D_ALLOC_OPEN, FALSE, NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage") + } /* end if */ + +done: + if(ret_value < 0) { + if(H5F_addr_defined(dataset->oloc.addr) && H5O_close(&(dataset->oloc), NULL) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") + if(dataset->shared) { + if(layout_init) + if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset, dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") + if(dataset->shared->space && H5S_close(dataset->shared->space) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") + if(dataset->shared->type) { + if(dataset->shared->type_id > 0) { + if(H5I_dec_ref(dataset->shared->type_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") + } /* end if */ + else { + if(H5T_close(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) +{ + hbool_t free_failed = FALSE; /* Set if freeing sub-components failed */ + hbool_t corked; /* Whether the dataset is corked or not */ + hbool_t file_closed = TRUE; /* H5O_close also closed the file? */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* check args */ + HDassert(dataset && dataset->oloc.file && dataset->shared); + HDassert(dataset->shared->fo_count > 0); + + /* Dump debugging info */ +#ifdef H5D_CHUNK_DEBUG + H5D__chunk_stats(dataset, FALSE); +#endif /* H5D_CHUNK_DEBUG */ + + dataset->shared->fo_count--; + if(dataset->shared->fo_count == 0) { + + /* Flush the dataset's information. Continue to close even if it fails. */ + if(H5D__flush_real(dataset, H5AC_ind_read_dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to flush cached dataset info") + + /* Set a flag to indicate the dataset is closing, before we start freeing things */ + /* (Avoids problems with flushing datasets twice, when one is holding + * the file open and it iterates through dataset to flush them -QAK) + */ + dataset->shared->closing = TRUE; + + /* Free cached information for each kind of dataset */ + switch(dataset->shared->layout.type) { + case H5D_CONTIGUOUS: + /* Free the data sieve buffer, if it's been allocated */ + if(dataset->shared->cache.contig.sieve_buf) + dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf); + break; + + case H5D_CHUNKED: + /* Check for skip list for iterating over chunks during I/O to close */ + if(dataset->shared->cache.chunk.sel_chunks) { + HDassert(H5SL_count(dataset->shared->cache.chunk.sel_chunks) == 0); + H5SL_close(dataset->shared->cache.chunk.sel_chunks); + dataset->shared->cache.chunk.sel_chunks = NULL; + } /* end if */ + + /* Check for cached single chunk dataspace */ + if(dataset->shared->cache.chunk.single_space) { + (void)H5S_close(dataset->shared->cache.chunk.single_space); + dataset->shared->cache.chunk.single_space = NULL; + } /* end if */ + + /* Check for cached single element chunk info */ + if(dataset->shared->cache.chunk.single_chunk_info) { + dataset->shared->cache.chunk.single_chunk_info = H5FL_FREE(H5D_chunk_info_t, dataset->shared->cache.chunk.single_chunk_info); + dataset->shared->cache.chunk.single_chunk_info = NULL; + } /* end if */ + break; + + case H5D_COMPACT: + /* Nothing special to do (info freed in the layout destroy) */ + break; + + case H5D_VIRTUAL: + { + size_t i, j; + + HDassert(dataset->shared->layout.storage.u.virt.list || (dataset->shared->layout.storage.u.virt.list_nused == 0)); + + /* Close source datasets */ + for(i = 0; i < dataset->shared->layout.storage.u.virt.list_nused; i++) { + /* Close source dataset */ + if(dataset->shared->layout.storage.u.virt.list[i].source_dset.dset) { + HDassert(dataset->shared->layout.storage.u.virt.list[i].source_dset.dset != dataset); + if(H5D_close(dataset->shared->layout.storage.u.virt.list[i].source_dset.dset) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to close source dataset") + dataset->shared->layout.storage.u.virt.list[i].source_dset.dset = NULL; + } /* end if */ + + /* Close sub datasets */ + for(j = 0; j < dataset->shared->layout.storage.u.virt.list[i].sub_dset_nused; j++) + if(dataset->shared->layout.storage.u.virt.list[i].sub_dset[j].dset) { + HDassert(dataset->shared->layout.storage.u.virt.list[i].sub_dset[j].dset != dataset); + if(H5D_close(dataset->shared->layout.storage.u.virt.list[i].sub_dset[j].dset) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to close source dataset") + dataset->shared->layout.storage.u.virt.list[i].sub_dset[j].dset = NULL; + } /* end if */ + } /* end for */ + } /* end block */ + break; + + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + default: + HDassert("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") +#endif /* NDEBUG */ + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + + /* Destroy any cached layout information for the dataset */ + if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset, H5AC_ind_read_dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") + + /* Free the external file prefix */ + dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix); + + /* Release layout, fill-value, efl & pipeline messages */ + if(dataset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT) + free_failed |= (H5O_msg_reset(H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline) < 0) || + (H5O_msg_reset(H5O_LAYOUT_ID, &dataset->shared->layout) < 0) || + (H5O_msg_reset(H5O_FILL_ID, &dataset->shared->dcpl_cache.fill) < 0) || + (H5O_msg_reset(H5O_EFL_ID, &dataset->shared->dcpl_cache.efl) < 0); + + /* Uncork cache entries with object address tag */ + if(H5AC_cork(dataset->oloc.file, dataset->oloc.addr, H5AC__GET_CORKED, &corked) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve an object's cork status") + if(corked) + if(H5AC_cork(dataset->oloc.file, dataset->oloc.addr, H5AC__UNCORK, NULL) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTUNCORK, FAIL, "unable to uncork an object") + + /* + * Release datatype, dataspace and creation property list -- there isn't + * much we can do if one of these fails, so we just continue. + */ + free_failed |= (H5I_dec_ref(dataset->shared->type_id) < 0) || + (H5S_close(dataset->shared->space) < 0) || + (H5I_dec_ref(dataset->shared->dcpl_id) < 0); + + /* Remove the dataset from the list of opened objects in the file */ + if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") + if(H5FO_delete(dataset->oloc.file, H5AC_ind_read_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), &file_closed) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") + + /* Evict dataset metadata if evicting on close */ + if(!file_closed && H5F_SHARED(dataset->oloc.file) && H5F_EVICT_ON_CLOSE(dataset->oloc.file)) { + if(H5AC_flush_tagged_metadata(dataset->oloc.file, dataset->oloc.addr, H5AC_ind_read_dxpl_id) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush tagged metadata") + if(H5AC_evict_tagged_metadata(dataset->oloc.file, dataset->oloc.addr, FALSE, H5AC_ind_read_dxpl_id) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to evict tagged metadata") + } /* end if */ + + /* + * Free memory. Before freeing the memory set the file pointer to NULL. + * We always check for a null file pointer in other H5D functions to be + * sure we're not accessing an already freed dataset (see the HDassert() + * above). + */ + dataset->oloc.file = NULL; + dataset->shared = H5FL_FREE(H5D_shared_t, dataset->shared); + + } /* end if */ + else { + /* Decrement the ref. count for this object in the top file */ + if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") + + /* Check reference count for this object in the top file */ + if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) { + if(H5O_close(&(dataset->oloc), NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to close") + } /* end if */ + else + /* Free object location (i.e. "unhold" the file if appropriate) */ + if(H5O_loc_free(&(dataset->oloc)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "problem attempting to free location") + } /* end else */ + + /* Release the dataset's path info */ + if(H5G_name_free(&(dataset->path)) < 0) + free_failed = TRUE; + + /* Free the dataset's memory structure */ + dataset = H5FL_FREE(H5D_t, dataset); + + /* Check if anything failed in the middle... */ + if(free_failed) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free a component of the dataset, but the dataset was freed anyway.") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_close() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_mult_refresh_close + * + * Purpose: Closing down the needed information when the dataset has + * multiple opens. (From H5O_refresh_metadata_close()) + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi + * 12/24/15 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_mult_refresh_close(hid_t dset_id, hid_t dxpl_id) +{ + H5D_t *dataset; /* Dataset to refresh */ + herr_t ret_value = SUCCEED; /* return value */ + + FUNC_ENTER_NOAPI(FAIL) + + if(NULL == (dataset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + + /* check args */ + HDassert(dataset && dataset->oloc.file && dataset->shared); + HDassert(dataset->shared->fo_count > 0); + + if(dataset->shared->fo_count > 1) { + /* Free cached information for each kind of dataset */ + switch(dataset->shared->layout.type) { + case H5D_CONTIGUOUS: + /* Free the data sieve buffer, if it's been allocated */ + if(dataset->shared->cache.contig.sieve_buf) + dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf); + break; + + case H5D_CHUNKED: + /* Check for skip list for iterating over chunks during I/O to close */ + if(dataset->shared->cache.chunk.sel_chunks) { + HDassert(H5SL_count(dataset->shared->cache.chunk.sel_chunks) == 0); + H5SL_close(dataset->shared->cache.chunk.sel_chunks); + dataset->shared->cache.chunk.sel_chunks = NULL; + } /* end if */ + + /* Check for cached single chunk dataspace */ + if(dataset->shared->cache.chunk.single_space) { + (void)H5S_close(dataset->shared->cache.chunk.single_space); + dataset->shared->cache.chunk.single_space = NULL; + } /* end if */ + + /* Check for cached single element chunk info */ + if(dataset->shared->cache.chunk.single_chunk_info) { + dataset->shared->cache.chunk.single_chunk_info = H5FL_FREE(H5D_chunk_info_t, dataset->shared->cache.chunk.single_chunk_info); + dataset->shared->cache.chunk.single_chunk_info = NULL; + } /* end if */ + break; + + case H5D_COMPACT: + case H5D_VIRTUAL: + /* Nothing special to do (info freed in the layout destroy) */ + break; + + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + default: + HDassert("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") +#endif /* NDEBUG */ + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + + /* Destroy any cached layout information for the dataset */ + if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_mult_refresh_close() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_mult_refresh_reopen + * + * Purpose: Re-initialize the needed info when the dataset has multiple + * opens. (From H5O_refresh_metadata_reopen()) + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi + * 12/24/15 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_mult_refresh_reopen(H5D_t *dataset, hid_t dxpl_id) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* check args */ + HDassert(dataset && dataset->oloc.file && dataset->shared); + HDassert(dataset->shared->fo_count > 0); + + if(dataset->shared->fo_count > 1) { + /* Release dataspace info */ + if(H5S_close(dataset->shared->space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + + /* Re-load dataspace info */ + if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc), dxpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header") + + /* Cache the dataset's dataspace info */ + if(H5D__cache_dataspace_info(dataset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't cache dataspace info") + + /* Release layout info */ + if(H5O_msg_reset(H5O_LAYOUT_ID, &dataset->shared->layout) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRESET, FAIL, "unable to reset layout info") + + /* Re-load layout message info */ + if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message") + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D_mult_refresh_reopen() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_oloc + * + * Purpose: Returns a pointer to the object location for a dataset. + * + * Return: Success: Ptr to location + * Failure: NULL + * + * 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_io_info_t *io_info, H5D_time_alloc_t time_alloc, + hbool_t full_overwrite, hsize_t old_dim[]) +{ + const H5D_t *dset = io_info->dset; /* The dataset object */ + H5F_t *f = dset->oloc.file; /* The dataset's file pointer */ + H5O_layout_t *layout; /* The dataset's layout information */ + hbool_t must_init_space = FALSE; /* Flag to indicate that space should be initialized */ + hbool_t addr_set = FALSE; /* Flag to indicate that the dataset's storage address was set */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* check args */ + HDassert(dset); + HDassert(f); + + /* If the data is stored in external files, don't set an address for the layout + * We assume that external storage is already + * allocated by the caller, or at least will be before I/O is performed. + */ + if(!(H5S_NULL == H5S_GET_EXTENT_TYPE(dset->shared->space) || dset->shared->dcpl_cache.efl.nused > 0)) { + /* Get a pointer to the dataset's layout information */ + layout = &(dset->shared->layout); + + switch(layout->type) { + case H5D_CONTIGUOUS: + if(!(*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { + /* Check if we have a zero-sized dataset */ + if(layout->storage.u.contig.size > 0) { + /* Reserve space in the file for the entire array */ + if(H5D__contig_alloc(f, io_info->md_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 index that manages chunked storage */ + if(H5D__chunk_create(dset /*in,out*/, io_info->md_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 + * index gets expanded. -QAK + */ + if(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY + && time_alloc == H5D_ALLOC_EXTEND) + must_init_space = TRUE; + break; + + case H5D_COMPACT: + /* Check if space is already allocated */ + if(NULL == layout->storage.u.compact.buf) { + /* Reserve space in layout header message for the entire array. + * Starting from the 1.8.7 release, we allow dataspace to have + * zero dimension size. So the storage size can be zero. + * SLU 2011/4/4 */ + if(layout->storage.u.compact.size > 0) { + if(NULL == (layout->storage.u.compact.buf = H5MM_malloc(layout->storage.u.compact.size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset") + if(!full_overwrite) + HDmemset(layout->storage.u.compact.buf, 0, layout->storage.u.compact.size); + layout->storage.u.compact.dirty = TRUE; + + /* Indicate that we should initialize storage space */ + must_init_space = TRUE; + } else { + layout->storage.u.compact.dirty = FALSE; + must_init_space = FALSE; + } + } /* end if */ + break; + + case H5D_VIRTUAL: + /* No-op, as the raw data is stored elsewhere and the global + * heap object containing the mapping information is created + * when the layout message is encoded. We may wish to move the + * creation of the global heap object here at some point, but we + * will have to make sure is it always created before the + * dataset is closed. */ + break; + + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + default: + HDassert("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") +#endif /* NDEBUG */ + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + + /* Check if we need to initialize the space */ + if(must_init_space) { + if(layout->type == H5D_CHUNKED) { + /* If we are doing incremental allocation and the index got + * created during a H5Dwrite call, don't initialize the storage + * now, wait for the actual writes to each block and let the + * low-level chunking routines handle initialize the fill-values. + * Otherwise, pass along the space initialization call and let + * the low-level chunking routines sort out whether to write + * fill values to the chunks they allocate space for. Yes, + * this is icky. -QAK + */ + if(!(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_INCR && time_alloc == H5D_ALLOC_WRITE)) + if(H5D__init_storage(io_info, full_overwrite, old_dim) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") + } /* end if */ + else { + H5D_fill_value_t fill_status; /* The fill value status */ + + /* Check the dataset's fill-value status */ + if(H5P_is_fill_value_defined(&dset->shared->dcpl_cache.fill, &fill_status) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") + + /* If we are filling the dataset on allocation or "if set" and + * the fill value _is_ set, do that now */ + if(dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || + (dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) + if(H5D__init_storage(io_info, full_overwrite, old_dim) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") + } /* end else */ + } /* end if */ + + /* If we set the address (and aren't in the middle of creating the + * dataset), mark the layout header message for later writing to + * the file. (this improves forward compatibility). + */ + /* (The layout message is already in the dataset's object header, this + * operation just sets the address and makes it constant) + */ + if(time_alloc != H5D_ALLOC_CREATE && addr_set) + /* Mark the layout as dirty, for later writing to the file */ + if(H5D__mark(dset, io_info->md_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_io_info_t *io_info, hbool_t full_overwrite, hsize_t old_dim[]) +{ + const H5D_t *dset = io_info->dset; /* dataset pointer */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + HDassert(dset); + + switch (dset->shared->layout.type) { + case H5D_COMPACT: + /* If we will be immediately overwriting the values, don't bother to clear them */ + if(!full_overwrite) { + /* Fill the compact dataset storage */ + if(H5D__compact_fill(dset, io_info->md_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(io_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") + break; + + case H5D_CHUNKED: + /* + * Allocate file space + * for all chunks now and initialize each chunk with the fill value. + */ + { + hsize_t zero_dim[H5O_LAYOUT_NDIMS] = {0}; + + /* Use zeros for old dimensions if not specified */ + if(old_dim == NULL) + old_dim = zero_dim; + + if(H5D__chunk_allocate(io_info, full_overwrite, old_dim) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") + break; + } /* end block */ + + case H5D_VIRTUAL: + /* No-op, as the raw data is stored elsewhere */ + + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + default: + HDassert("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") +#endif /* NDEBUG */ + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__init_storage() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__get_storage_size + * + * Purpose: Determines how much space has been reserved to store the raw + * data of a dataset. + * + * Return: Non-negative on success, negative on failure + * + * 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_VIRTUAL: + /* Just set to 0, as virtual datasets do not actually store raw data + */ + *storage_size = 0; + break; + + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + default: + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset type") + } /*lint !e788 All appropriate cases are covered */ + +done: + FUNC_LEAVE_NOAPI_TAG(ret_value, 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_VIRTUAL: + case H5D_CHUNKED: + case H5D_COMPACT: + break; + + case H5D_CONTIGUOUS: + /* If dataspace hasn't been allocated or dataset is stored in + * an external file, the value will be HADDR_UNDEF. */ + if(dset->shared->dcpl_cache.efl.nused == 0 || H5F_addr_defined(dset->shared->layout.storage.u.contig.addr)) + /* Return the absolute dataset offset from the beginning of file. */ + ret_value = dset->shared->layout.storage.u.contig.addr + H5F_BASE_ADDR(dset->oloc.file); + break; + + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + default: + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "unknown dataset layout type") + } /*lint !e788 All appropriate cases are covered */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__get_offset() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_vlen_reclaim + * + * Purpose: Frees the buffers allocated for storing variable-length data + * in memory. Only frees the VL data in the selection defined in the + * dataspace. 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_t *type; /* Datatype */ + H5S_sel_iter_op_t dset_op; /* Operator for iteration */ + 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 = FAIL; /* Return 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); + + if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype") + + /* Get the allocation info */ + if(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 H5S_select_iterate with args, etc. */ + dset_op.op_type = H5S_SEL_ITER_OP_APP; + dset_op.u.app_op.op = H5T_vlen_reclaim; + dset_op.u.app_op.type_id = type_id; + + ret_value = H5S_select_iterate(buf, type, space, &dset_op, vl_alloc_info); + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_vlen_reclaim() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__vlen_get_buf_size_alloc + * + * Purpose: This routine makes certain there is enough space in the temporary + * buffer for the new data to read in. All the VL data read in is actually + * placed in this buffer, overwriting the previous data. Needless to say, + * this data is not actually usable. + * + * Return: Non-negative on success, negative on failure + * + * 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 = NULL; /* Return value */ + + FUNC_ENTER_PACKAGE_NOERR + + /* Get a temporary pointer to space for the VL data */ + if((vlen_bufsize->vl_tbuf = H5FL_BLK_REALLOC(vlen_vl_buf, vlen_bufsize->vl_tbuf, size)) != NULL) + vlen_bufsize->size += size; + + /* Set return value */ + ret_value = vlen_bufsize->vl_tbuf; + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__vlen_get_buf_size_alloc() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__vlen_get_buf_size + * + * Purpose: This routine checks the number of bytes required to store a single + * element from a dataset in memory, creating a selection with just the + * single element selected to read in the element and using a custom memory + * allocator for any VL data encountered. + * The *size value is modified according to how many bytes are + * required to store the element in memory. + * + * Implementation: This routine actually performs the read with a custom + * memory manager which basically just counts the bytes requested and + * uses a temporary memory buffer (through the H5FL API) to make certain + * enough space is available to perform the read. Then the temporary + * buffer is released and the number of bytes allocated is returned. + * Kinda kludgy, but easier than the other method of trying to figure out + * the sizes without actually reading the data in... - QAK + * + * Return: Non-negative on success, negative on failure + * + * Programmer: Quincey Koziol + * Tuesday, August 17, 1999 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D__vlen_get_buf_size(void H5_ATTR_UNUSED *elem, hid_t type_id, unsigned H5_ATTR_UNUSED ndim, const hsize_t *point, void *op_data) +{ + H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)op_data; + H5T_t *dt; /* Datatype for operation */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + HDassert(op_data); + HDassert(H5I_DATATYPE == H5I_get_type(type_id)); + + /* Check args */ + if(NULL == (dt = (H5T_t *)H5I_object(type_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not a datatype") + + /* Make certain there is enough fixed-length buffer available */ + if(NULL == (vlen_bufsize->fl_tbuf = H5FL_BLK_REALLOC(vlen_fl_buf, vlen_bufsize->fl_tbuf, H5T_get_size(dt)))) + HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, FAIL, "can't resize tbuf") + + /* Select point to read in */ + if(H5S_select_elements(vlen_bufsize->fspace, H5S_SELECT_SET, (size_t)1, point) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't select point") + + /* Read in the point (with the custom VL memory allocator) */ + if(H5D__read(vlen_bufsize->dset, type_id, vlen_bufsize->mspace, vlen_bufsize->fspace, vlen_bufsize->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) +{ + hsize_t curr_dims[H5S_MAX_RANK]; /* Current dimension sizes */ + htri_t changed; /* Whether the dataspace changed size */ + size_t u, v; /* Local index variable */ + 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") + + /* Keep the current dataspace dimensions for later */ + HDcompile_assert(sizeof(curr_dims) == sizeof(dset->shared->curr_dims)); + HDmemcpy(curr_dims, dset->shared->curr_dims, H5S_MAX_RANK * sizeof(curr_dims[0])); + + /* Modify the size of the dataspace */ + if((changed = H5S_set_extent(dset->shared->space, size)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") + + /* Don't bother updating things, unless they've changed */ + if(changed) { + hbool_t shrink = FALSE; /* Flag to indicate a dimension has shrank */ + hbool_t expand = FALSE; /* Flag to indicate a dimension has grown */ + hbool_t update_chunks = FALSE; /* Flag to indicate chunk cache update is needed */ + + /* Determine if we are shrinking and/or expanding any dimensions */ + for(u = 0; u < (size_t)dset->shared->ndims; u++) { + /* Check for various status changes */ + if(size[u] < curr_dims[u]) + shrink = TRUE; + if(size[u] > curr_dims[u]) + expand = TRUE; + + /* Chunked storage specific checks */ + if(H5D_CHUNKED == dset->shared->layout.type && dset->shared->ndims > 1) { + hsize_t scaled; /* Scaled value */ + + /* Compute the scaled dimension size value */ + scaled = size[u] / dset->shared->layout.u.chunk.dim[u]; + + /* Check if scaled dimension size changed */ + if(scaled != dset->shared->cache.chunk.scaled_dims[u]) { + hsize_t scaled_power2up; /* Scaled value, rounded to next power of 2 */ + + /* Update the scaled dimension size value for the current dimension */ + dset->shared->cache.chunk.scaled_dims[u] = scaled; + + /* Check if algorithm for computing hash values will change */ + if((scaled > dset->shared->cache.chunk.nslots && + dset->shared->cache.chunk.scaled_dims[u] <= dset->shared->cache.chunk.nslots) + || (scaled <= dset->shared->cache.chunk.nslots && + dset->shared->cache.chunk.scaled_dims[u] > dset->shared->cache.chunk.nslots)) + update_chunks = TRUE; + + /* Check if the number of bits required to encode the scaled size value changed */ + if(dset->shared->cache.chunk.scaled_power2up[u] != (scaled_power2up = H5VM_power2up(scaled))) { + /* Update the 'power2up' & 'encode_bits' values for the current dimension */ + dset->shared->cache.chunk.scaled_power2up[u] = scaled_power2up; + dset->shared->cache.chunk.scaled_encode_bits[u] = H5VM_log2_gen(scaled_power2up); + + /* Indicate that the cached chunk indices need to be updated */ + update_chunks = TRUE; + } /* end if */ + } /* end if */ + } /* end if */ + + /* Update the cached copy of the dataset's dimensions */ + dset->shared->curr_dims[u] = size[u]; + } /* end for */ + + /*------------------------------------------------------------------------- + * Modify the dataset storage + *------------------------------------------------------------------------- + */ + /* Update the index values for the cached chunks for this dataset */ + if(H5D_CHUNKED == dset->shared->layout.type) { + /* Set the cached chunk info */ + if(H5D__chunk_set_info(dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to update # of chunks") + + /* Check if updating the chunk cache indices is necessary */ + if(update_chunks) + /* Update the chunk cache indices */ + if(H5D__chunk_update_cache(dset, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices") + } /* end if */ + + /* Operations for virtual datasets */ + if(H5D_VIRTUAL == dset->shared->layout.type) { + /* Check that the dimensions of the VDS are large enough */ + if(H5D_virtual_check_min_dims(dset) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "virtual dataset dimensions not large enough to contain all limited dimensions in all selections") + + /* Patch the virtual selection dataspaces */ + for(u = 0; u < dset->shared->layout.storage.u.virt.list_nused; u++) { + /* Patch extent */ + if(H5S_set_extent(dset->shared->layout.storage.u.virt.list[u].source_dset.virtual_select, size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + dset->shared->layout.storage.u.virt.list[u].virtual_space_status = H5O_VIRTUAL_STATUS_CORRECT; + + /* Patch sub-source datasets */ + for(v = 0; v < dset->shared->layout.storage.u.virt.list[u].sub_dset_nalloc; v++) + if(H5S_set_extent(dset->shared->layout.storage.u.virt.list[u].sub_dset[v].virtual_select, size) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + } /* end for */ + + /* Mark virtual datasets as not fully initialized so internal + * selections are recalculated (at next I/O operation) */ + dset->shared->layout.storage.u.virt.init = FALSE; + } /* end if */ + + /* Allocate space for the new parts of the dataset, if appropriate */ + if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY) { + H5D_io_info_t io_info; + + io_info.dset = dset; + io_info.raw_dxpl_id = H5AC_rawdata_dxpl_id; + io_info.md_dxpl_id = dxpl_id; + + if(H5D__alloc_storage(&io_info, H5D_ALLOC_EXTEND, FALSE, curr_dims) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to extend dataset storage") + } + /*------------------------------------------------------------------------- + * Remove chunk information in the case of chunked datasets + * This removal takes place only in case we are shrinking the dateset + * and if the chunks are written + *------------------------------------------------------------------------- + */ + if(H5D_CHUNKED == dset->shared->layout.type) { + if(shrink && (*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) + /* Remove excess chunks */ + if(H5D__chunk_prune_by_extent(dset, dxpl_id, curr_dims) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks") + + /* Update chunks that are no longer edge chunks as a result of + * expansion */ + if(expand && (dset->shared->layout.u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) + && (dset->shared->dcpl_cache.pline.nused > 0)) + if(H5D__chunk_update_old_edge_chunks(dset, dxpl_id, curr_dims) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to do update old edge chunks") + } /* end if */ + + /* Mark the dataspace as dirty, for later writing to the file */ + if(H5D__mark(dset, 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) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE_TAG(dxpl_id, dataset->oloc.addr, FAIL) + + /* Check args */ + HDassert(dataset); + HDassert(dataset->shared); + + /* Avoid flushing the dataset (again) if it's closing */ + if(!dataset->shared->closing) { + /* Flush cached raw data for each kind of dataset layout */ + if(dataset->shared->layout.ops->flush && + (dataset->shared->layout.ops->flush)(dataset, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush raw data") + } /* end if */ + +done: + FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL) +} /* end H5D__flush_real() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__format_convert + * + * Purpose: For chunked: downgrade the chunk indexing type to version 1 B-tree + * For compact/contiguous: downgrade layout version to 3 + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Vailin Choi + * Feb 2015 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D__format_convert(H5D_t *dataset, hid_t dxpl_id) +{ + H5D_chk_idx_info_t new_idx_info; /* Index info for the new layout */ + H5D_chk_idx_info_t idx_info; /* Index info for the current layout */ + H5O_layout_t newlayout; /* The new layout */ + hbool_t init_new_index = FALSE; /* Indicate that the new chunk index is initialized */ + hbool_t delete_old_layout = FALSE; /* Indicate that the old layout message is deleted */ + hbool_t add_new_layout = FALSE; /* Indicate that the new layout message is added */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE_TAG(dxpl_id, dataset->oloc.addr, FAIL) + + /* Check args */ + HDassert(dataset); + + switch(dataset->shared->layout.type) { + case H5D_CHUNKED: + HDassert(dataset->shared->layout.u.chunk.idx_type != H5D_CHUNK_IDX_BTREE); + + /* Set up the current index info */ + idx_info.f = dataset->oloc.file; + idx_info.dxpl_id = dxpl_id; + idx_info.pline = &dataset->shared->dcpl_cache.pline; + idx_info.layout = &dataset->shared->layout.u.chunk; + idx_info.storage = &dataset->shared->layout.storage.u.chunk; + + /* Copy the current layout info to the new layout */ + HDmemcpy(&newlayout, &dataset->shared->layout, sizeof(H5O_layout_t)); + + /* Set up info for version 1 B-tree in the new layout */ + newlayout.version = H5O_LAYOUT_VERSION_3; + newlayout.storage.u.chunk.idx_type = H5D_CHUNK_IDX_BTREE; + newlayout.storage.u.chunk.idx_addr = HADDR_UNDEF; + newlayout.storage.u.chunk.ops = H5D_COPS_BTREE; + newlayout.storage.u.chunk.u.btree.shared = NULL; + + /* Set up the index info to version 1 B-tree */ + new_idx_info.f = dataset->oloc.file; + new_idx_info.dxpl_id = dxpl_id; + new_idx_info.pline = &dataset->shared->dcpl_cache.pline; + new_idx_info.layout = &newlayout.u.chunk; + new_idx_info.storage = &newlayout.storage.u.chunk; + + /* Initialize version 1 B-tree */ + if(new_idx_info.storage->ops->init && + (new_idx_info.storage->ops->init)(&new_idx_info, dataset->shared->space, dataset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize indexing information") + init_new_index = TRUE; + + /* If the current chunk index exists */ + if(H5F_addr_defined(idx_info.storage->idx_addr)) { + + /* Create v1 B-tree chunk index */ + if((new_idx_info.storage->ops->create)(&new_idx_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create chunk index") + + /* Iterate over the chunks in the current index and insert the chunk addresses + * into the version 1 B-tree chunk index */ + if(H5D__chunk_format_convert(dataset, &idx_info, &new_idx_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate/convert chunk index") + } /* end if */ + + /* Delete the old "current" layout message */ + if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, FALSE, dxpl_id) < 0) + HGOTO_ERROR(H5E_SYM, H5E_CANTDELETE, FAIL, "unable to delete layout message") + + delete_old_layout = TRUE; + + /* Append the new layout message to the object header */ + if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &newlayout, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout header message") + + add_new_layout = TRUE; + + /* Release the old (current) chunk index */ + if(idx_info.storage->ops->dest && (idx_info.storage->ops->dest)(&idx_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info") + + /* Copy the new layout to the dataset's layout */ + HDmemcpy(&dataset->shared->layout, &newlayout, sizeof(H5O_layout_t)); + + break; + + case H5D_CONTIGUOUS: + case H5D_COMPACT: + HDassert(dataset->shared->layout.version > H5O_LAYOUT_VERSION_DEFAULT); + dataset->shared->layout.version = H5O_LAYOUT_VERSION_DEFAULT; + if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), dxpl_id) < 0) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") + break; + + case H5D_VIRTUAL: + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "virtual dataset layout not supported") + + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset layout type") + + default: + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "unknown dataset layout type") + } /* end switch */ + +done: + if(ret_value < 0 && dataset->shared->layout.type == H5D_CHUNKED) { + /* Remove new layout message */ + if(add_new_layout) + if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, FALSE, dxpl_id) < 0) + HDONE_ERROR(H5E_SYM, H5E_CANTDELETE, FAIL, "unable to delete layout message") + + /* Add back old layout message */ + if(delete_old_layout) + if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &dataset->shared->layout, dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to add layout header message") + + /* Clean up v1 b-tree chunk index */ + if(init_new_index) { + if(H5F_addr_defined(new_idx_info.storage->idx_addr)) { + /* Check for valid address i.e. tag */ + if(!H5F_addr_defined(dataset->oloc.addr)) + HDONE_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "address undefined") + + /* Expunge from cache all v1 B-tree type entries associated with tag */ + if(H5AC_expunge_tag_type_metadata(dataset->oloc.file, dxpl_id, dataset->oloc.addr, H5AC_BT_ID, H5AC__NO_FLAGS_SET)) + HDONE_ERROR(H5E_DATASET, H5E_CANTEXPUNGE, FAIL, "unable to expunge index metadata") + } /* end if */ + + /* Delete v1 B-tree chunk index */ + if(new_idx_info.storage->ops->dest && (new_idx_info.storage->ops->dest)(&new_idx_info) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info") + } /* end if */ + } /* end if */ + + FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL) +} /* end H5D__format_convert() */ + + +/*------------------------------------------------------------------------- + * 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 H5_ATTR_UNUSED dxpl_id, unsigned flags) +{ + H5O_t *oh = NULL; /* Pointer to dataset's object header */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check args */ + HDassert(dataset); + HDassert(!(flags & (unsigned)~(H5D_MARK_SPACE | H5D_MARK_LAYOUT))); + + /* Mark aspects of the dataset as dirty */ + if(flags) { + unsigned update_flags = H5O_UPDATE_TIME; /* Modification time flag */ + + /* Pin the object header */ + if(NULL == (oh = H5O_pin(&dataset->oloc, 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(flags & H5D_MARK_LAYOUT) { + if(H5D__layout_oh_write(dataset, dxpl_id, oh, update_flags) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout info") + + /* Reset the "update the modification time" flag, so we only do it once */ + update_flags = 0; + } /* end if */ + + /* Update the dataspace on disk, if it's been changed */ + if(flags & H5D_MARK_SPACE) { + if(H5S_write(dataset->oloc.file, dxpl_id, oh, update_flags, dataset->shared->space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") + + /* Reset the "update the modification time" flag, so we only do it once */ + update_flags = 0; + } /* end if */ + + /* _Somebody_ should have update the modification time! */ + HDassert(update_flags == 0); + } /* end if */ + +done: + /* Release pointer to object header */ + if(oh != NULL) + if(H5O_unpin(oh) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTUNPIN, FAIL, "unable to unpin dataset object header") + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__mark() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__flush_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 H5_ATTR_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_layout_t copied_layout; /* Layout to tweak */ + H5O_fill_t copied_fill; /* Fill value to tweak */ + H5O_efl_t copied_efl; /* External file list to tweak */ + hid_t new_dcpl_id = FAIL; + hid_t ret_value = H5I_INVALID_HID; /* Return value */ + + FUNC_ENTER_NOAPI(FAIL) + + /* Check args */ + if(NULL == (dcpl_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get property list") + + /* Copy the creation property list */ + if((new_dcpl_id = H5P_copy_plist(dcpl_plist, TRUE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to copy the creation property list") + if(NULL == (new_plist = (H5P_genplist_t *)H5I_object(new_dcpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get property list") + + /* Retrieve any object creation properties */ + if(H5O_get_create_plist(&dset->oloc, H5AC_ind_read_dxpl_id, new_plist) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get object creation info") + + /* Get the layout property */ + if(H5P_peek(new_plist, H5D_CRT_LAYOUT_NAME, &copied_layout) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get layout") + + /* Reset layout values set when dataset is created */ + copied_layout.ops = NULL; + switch(copied_layout.type) { + case H5D_COMPACT: + copied_layout.storage.u.compact.buf = H5MM_xfree(copied_layout.storage.u.compact.buf); + HDmemset(&copied_layout.storage.u.compact, 0, sizeof(copied_layout.storage.u.compact)); + break; + + case H5D_CONTIGUOUS: + copied_layout.storage.u.contig.addr = HADDR_UNDEF; + copied_layout.storage.u.contig.size = 0; + break; + + case H5D_CHUNKED: + /* Reset chunk size */ + copied_layout.u.chunk.size = 0; + + /* Reset index info, if the chunk ops are set */ + if(copied_layout.storage.u.chunk.ops) + /* Reset address and pointer of the array struct for the chunked storage index */ + if(H5D_chunk_idx_reset(&copied_layout.storage.u.chunk, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to reset chunked storage index in dest") + + /* Reset chunk index ops */ + copied_layout.storage.u.chunk.ops = NULL; + break; + + case H5D_VIRTUAL: + copied_layout.storage.u.virt.serial_list_hobjid.addr = HADDR_UNDEF; + copied_layout.storage.u.virt.serial_list_hobjid.idx = 0; + break; + + case H5D_LAYOUT_ERROR: + case H5D_NLAYOUTS: + default: + HDassert(0 && "Unknown layout type!"); + } /* end switch */ + + /* Set back the (possibly modified) layout property to property list */ + if(H5P_poke(new_plist, H5D_CRT_LAYOUT_NAME, &copied_layout) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set layout") + + /* Get the fill value property */ + if(H5P_peek(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value") + + /* Check if there is a fill value, but no type yet */ + if(copied_fill.buf != NULL && copied_fill.type == NULL) { + H5T_path_t *tpath; /* Conversion information*/ + + /* Copy the dataset type into the fill value message */ + if(NULL == (copied_fill.type = H5T_copy(dset->shared->type, H5T_COPY_TRANSIENT))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy dataset datatype for fill value") + + /* Set up type conversion function */ + if(NULL == (tpath = H5T_path_find(dset->shared->type, copied_fill.type, NULL, NULL, H5AC_noio_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_DATASET, H5E_CANTINIT, FAIL, "unable to copy/register datatype") + } /* end if */ + + /* Allocate a background buffer */ + bkg_size = MAX(H5T_GET_SIZE(copied_fill.type), H5T_GET_SIZE(dset->shared->type)); + if(H5T_path_bkg(tpath) && NULL == (bkg_buf = H5FL_BLK_CALLOC(type_conv, bkg_size))) { + H5I_dec_ref(src_id); + H5I_dec_ref(dst_id); + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "memory allocation failed") + } /* end if */ + + /* Convert fill value */ + if(H5T_convert(tpath, src_id, dst_id, (size_t)1, (size_t)0, (size_t)0, copied_fill.buf, bkg_buf, H5AC_noio_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 (possibly modified) fill value property to property list */ + if(H5P_poke(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set fill value") + + /* Get the fill value property */ + if(H5P_peek(new_plist, H5D_CRT_EXT_FILE_LIST_NAME, &copied_efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get external file list") + + /* Reset efl name_offset and heap_addr, these are the values when the dataset is created */ + if(copied_efl.slot) { + unsigned u; + + copied_efl.heap_addr = HADDR_UNDEF; + for(u = 0; u < copied_efl.nused; u++) + copied_efl.slot[u].name_offset = 0; + } /* end if */ + + /* Set back the (possibly modified) external file list property to property list */ + if(H5P_poke(new_plist, H5D_CRT_EXT_FILE_LIST_NAME, &copied_efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set external file list") + + /* Set the return value */ + ret_value = new_dcpl_id; + +done: + if(ret_value < 0) + if(new_dcpl_id > 0) + if(H5I_dec_app_ref(new_dcpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to close temporary object") + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_get_create_plist() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_get_access_plist + * + * Purpose: Returns a copy of the dataset access property list. + * + * Return: Success: ID for a copy of the dataset access + * property list. + * + * Failure: FAIL + * + * 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 & append flush parameters */ + if(dset->shared->layout.type == H5D_CHUNKED) { + if(H5P_set(new_plist, H5D_ACS_DATA_CACHE_NUM_SLOTS_NAME, &(dset->shared->cache.chunk.nslots)) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set data cache number of slots") + if(H5P_set(new_plist, H5D_ACS_DATA_CACHE_BYTE_SIZE_NAME, &(dset->shared->cache.chunk.nbytes_max)) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set data cache byte size") + if(H5P_set(new_plist, H5D_ACS_PREEMPT_READ_CHUNKS_NAME, &(dset->shared->cache.chunk.w0)) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set preempt read chunks") + if(H5P_set(new_plist, H5D_ACS_APPEND_FLUSH_NAME, &dset->shared->append_flush) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set append flush property") + } /* end if */ + + /* Set the VDS view & printf gap options */ + if(H5P_set(new_plist, H5D_ACS_VDS_VIEW_NAME, &(dset->shared->layout.storage.u.virt.view)) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set VDS view") + if(H5P_set(new_plist, H5D_ACS_VDS_PRINTF_GAP_NAME, &(dset->shared->layout.storage.u.virt.printf_gap)) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set VDS printf gap") + + /* Set the external file prefix option */ + if(H5P_set(new_plist, H5D_ACS_EFILE_PREFIX_NAME, &(dset->shared->extfile_prefix)) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set external file prefix") + + /* Set the return value */ + ret_value = new_dapl_id; + +done: + if(ret_value < 0) { + if(new_dapl_id > 0) + if(H5I_dec_app_ref(new_dapl_id) < 0) + HDONE_ERROR(H5E_SYM, H5E_CANTDEC, FAIL, "can't free") + } /* 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 = H5I_INVALID_HID; + + FUNC_ENTER_NOAPI_NOINIT + + /* If the layout is virtual, update the extent */ + if(dset->shared->layout.type == H5D_VIRTUAL) + if(H5D__virtual_set_extent_unlim(dset, H5AC_ind_read_dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update virtual dataset extent") + + /* 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() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__refresh + * + * Purpose: Refreshes all buffers associated with a dataset. + * + * Return: SUCCEED/FAIL + * + * Programmer: Dana Robinson + * November 2015 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D__refresh(hid_t dset_id, H5D_t *dset, hid_t dxpl_id) +{ + H5D_virtual_held_file_t *head = NULL; /* Pointer to list of files held open */ + hbool_t virt_dsets_held = FALSE; /* Whether virtual datasets' files are held open */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* Sanity check */ + HDassert(dset); + HDassert(dset->shared); + + /* If the layout is virtual... */ + if(dset->shared->layout.type == H5D_VIRTUAL) { + /* Hold open the source datasets' files */ + if(H5D__virtual_hold_source_dset_files(dset, &head) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "unable to hold VDS source files open") + virt_dsets_held = TRUE; + + /* Refresh source datasets for virtual dataset */ + if(H5D__virtual_refresh_source_dsets(dset, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to refresh VDS source datasets") + } /* end if */ + + /* Refresh dataset object */ + if((H5O_refresh_metadata(dset_id, dset->oloc, dxpl_id)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to refresh dataset") + +done: + /* Release hold on virtual datasets' files */ + if(virt_dsets_held) { + /* Release the hold on source datasets' files */ + if(H5D__virtual_release_source_dset_files(head) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't release VDS source files held open") + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__refresh() */ + |