diff options
Diffstat (limited to 'src/H5Dint.c')
| -rw-r--r-- | src/H5Dint.c | 2246 |
1 files changed, 1267 insertions, 979 deletions
diff --git a/src/H5Dint.c b/src/H5Dint.c index 3b938e2..c063bb9 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -21,14 +21,17 @@ /***********/ /* 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 */ +#include "H5private.h" /* Generic Functions */ +#include "H5CXprivate.h" /* API Contexts */ +#include "H5Dpkg.h" /* Datasets */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5Fprivate.h" /* Files */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5FOprivate.h" /* File objects */ +#include "H5Iprivate.h" /* IDs */ +#include "H5Lprivate.h" /* Links */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5VLprivate.h" /* Virtual Object Layer */ /****************/ @@ -40,11 +43,34 @@ /* Local Typedefs */ /******************/ -/* Struct for holding callback info during H5D_flush operation */ +/* Shared data structure for computing variable-length dataset's total size */ +/* (Used for both native and generic 'get vlen buf size' 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; + void *fl_tbuf; /* Ptr to the temporary buffer we are using for fixed-length data */ + void *vl_tbuf; /* Ptr to the temporary buffer we are using for VL data */ + size_t vl_tbuf_size; /* Current size of the temp. buffer for VL data */ + hsize_t size; /* Accumulated number of bytes for the selection */ +} H5D_vlen_bufsize_common_t; + +/* Internal data structure for computing variable-length dataset's total size */ +/* (Used for native 'get vlen buf size' operation) */ +typedef struct { + H5D_t *dset; /* Dataset for operation */ + H5S_t *fspace; /* Dataset's dataspace for operation */ + H5S_t *mspace; /* Memory dataspace for operation */ + H5D_vlen_bufsize_common_t common; /* VL data buffers & accumulatd size */ +} H5D_vlen_bufsize_native_t; + +/* Internal data structure for computing variable-length dataset's total size */ +/* (Used for generic 'get vlen buf size' operation) */ +typedef struct { + H5VL_object_t *dset_vol_obj; /* VOL object for the dataset */ + hid_t fspace_id; /* Dataset dataspace ID of the dataset we are working on */ + H5S_t *fspace; /* Dataset's dataspace for operation */ + hid_t mspace_id; /* Memory dataspace ID of the dataset we are working on */ + hid_t dxpl_id; /* Dataset transfer property list to pass to dataset read */ + H5D_vlen_bufsize_common_t common; /* VL data buffers & accumulatd size */ +} H5D_vlen_bufsize_generic_t; /********************/ @@ -52,29 +78,31 @@ typedef struct { /********************/ /* 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 H5D_shared_t *H5D__new(hid_t dcpl_id, hid_t dapl_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__update_oh_info(H5F_t *file, H5D_t *dset, hid_t dapl_id); +static herr_t H5D__build_file_prefix(const H5D_t *dset, H5F_prefix_open_t prefix_type, char **file_prefix); +static herr_t H5D__open_oid(H5D_t *dataset, hid_t dapl_id); static herr_t H5D__init_storage(const H5D_io_info_t *io_info, hbool_t full_overwrite, - hsize_t old_dim[]); + hsize_t old_dim[]); static herr_t H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id); +static herr_t H5D__close_cb(H5VL_object_t *dset_vol_obj); +static herr_t H5D__use_minimized_dset_headers(H5F_t *file, hbool_t *minimize); +static herr_t H5D__prepare_minimized_oh(H5F_t *file, H5D_t *dset, H5O_loc_t *oloc); +static size_t H5D__calculate_minimum_header_size(H5F_t *file, H5D_t *dset, H5O_t *ohdr); +static void *H5D__vlen_get_buf_size_alloc(size_t size, void *info); +static herr_t H5D__vlen_get_buf_size_cb(void *elem, hid_t type_id, unsigned ndim, + const hsize_t *point, void *op_data); +static herr_t H5D__vlen_get_buf_size_gen_cb(void *elem, hid_t type_id, unsigned ndim, + const hsize_t *point, void *op_data); + /*********************/ /* 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); @@ -104,34 +132,37 @@ H5FL_EXTERN(H5D_chunk_info_t); /* Declare extern the free list to manage blocks of type conversion data */ H5FL_BLK_EXTERN(type_conv); +/* Disable warning for intentional identical branches here -QAK */ +H5_GCC_DIAG_OFF(larger-than=) /* Define a static "default" dataset structure to use to initialize new datasets */ static H5D_shared_t H5D_def_dset; +H5_GCC_DIAG_ON(larger-than=) /* 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 */ + H5I_DATASET, /* ID class value */ + 0, /* Class flags */ + 0, /* # of reserved IDs for class */ + (H5I_free_t)H5D__close_cb /* Callback routine for closing objects of this class */ }}; /* Flag indicating "top" of interface has been initialized */ static hbool_t H5D_top_package_initialize_s = FALSE; +/* Prefixes of VDS and external file from the environment variables + * HDF5_EXTFILE_PREFIX and HDF5_VDS_PREFIX */ +static const char *H5D_prefix_ext_env = NULL; +static const char *H5D_prefix_vds_env = NULL; /*------------------------------------------------------------------------- - * Function: H5D_init + * Function: H5D_init * - * Purpose: Initialize the interface from some other layer. + * Purpose: Initialize the interface from some other layer. * - * Return: Success: non-negative - * - * Failure: negative - * - * Programmer: Quincey Koziol - * Saturday, March 4, 2000 + * Return: Success: non-negative * + * Failure: negative *------------------------------------------------------------------------- */ herr_t @@ -149,7 +180,7 @@ done: /*-------------------------------------------------------------------------- NAME - H5D__init_package -- Initialize interface-specific information + H5D__init_package -- Initialize interface-specific information USAGE herr_t H5D__init_package() @@ -176,6 +207,9 @@ H5D__init_package(void) /* Reset the "default dataset" information */ HDmemset(&H5D_def_dset, 0, sizeof(H5D_shared_t)); + H5D_def_dset.type_id = H5I_INVALID_HID; + H5D_def_dset.dapl_id = H5I_INVALID_HID; + H5D_def_dset.dcpl_id = H5I_INVALID_HID; /* Get the default dataset creation property list values and initialize the * default dataset with them. @@ -195,44 +229,37 @@ H5D__init_package(void) 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; + /* Retrieve the prefixes of VDS and external file from the environment variable */ + H5D_prefix_vds_env = HDgetenv("HDF5_VDS_PREFIX"); + H5D_prefix_ext_env = HDgetenv("HDF5_EXTFILE_PREFIX"); + 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. + * Function: H5D_top_term_package * - * Programmer: Quincey Koziol - * Sunday, September 13, 2015 + * Purpose: Close the "top" of the interface, releasing IDs, etc. * + * Return: Success: Positive if anything was done that might + * affect other interfaces; zero otherwise. + * Failure: Negative. *------------------------------------------------------------------------- */ int H5D_top_term_package(void) { - int n = 0; + int n = 0; FUNC_ENTER_NOAPI_NOINIT_NOERR if(H5D_top_package_initialize_s) { - if(H5I_nmembers(H5I_DATASET) > 0) { + 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 @@ -255,9 +282,9 @@ H5D_top_term_package(void) * * QAK - 5/13/03 */ - (void)H5I_clear_type(H5I_DATASET, TRUE, FALSE); + (void)H5I_clear_type(H5I_DATASET, TRUE, FALSE); n++; /*H5I*/ - } /* end if */ + } /* end if */ /* Mark closed */ if(0 == n) @@ -269,26 +296,22 @@ H5D_top_term_package(void) /*------------------------------------------------------------------------- - * Function: H5D_term_package - * - * Purpose: Terminate this interface. - * - * Note: Finishes shutting down the interface, after - * H5D_top_term_package() is called + * Function: H5D_term_package * - * Return: Success: Positive if anything was done that might - * affect other interfaces; zero otherwise. - * Failure: Negative. + * Purpose: Terminate this interface. * - * Programmer: Robb Matzke - * Friday, November 20, 1998 + * Note: Finishes shutting down the interface, after + * H5D_top_term_package() is called * + * Return: Success: Positive if anything was done that might + * affect other interfaces; zero otherwise. + * Failure: Negative. *------------------------------------------------------------------------- */ int H5D_term_package(void) { - int n = 0; + int n = 0; FUNC_ENTER_NOAPI_NOINIT_NOERR @@ -309,158 +332,60 @@ H5D_term_package(void) } /* 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 ---------------------------------------------------------------------------*/ +/*------------------------------------------------------------------------- + * Function: H5D__close_cb + * + * Purpose: Called when the ref count reaches zero on the dataset's ID + * + * Return: SUCCEED/FAIL + * + *------------------------------------------------------------------------- + */ static herr_t -H5D__get_dxpl_cache_real(hid_t dxpl_id, H5D_dxpl_cache_t *cache) +H5D__close_cb(H5VL_object_t *dset_vol_obj) { - H5P_genplist_t *dx_plist; /* Data transfer property list */ - herr_t ret_value = SUCCEED; /* Return value */ + 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 */ + /* Sanity check */ + HDassert(dset_vol_obj); - FUNC_ENTER_PACKAGE + /* Close the dataset */ + if(H5VL_dataset_close(dset_vol_obj, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to close dataset"); - /* Check args */ - HDassert(cache); +done: + /* XXX: (MSC) Weird thing for datasets and filters: + * Always decrement the ref count on the VOL for datasets, since + * the ID is removed even if the close fails. + */ - /* 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") + /* Free the VOL object */ + if(H5VL_free_object(dset_vol_obj) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to free VOL object"); -done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5D__get_dxpl_cache() */ +} /* end H5D__close_cb() */ /*------------------------------------------------------------------------- - * Function: H5D__create_named - * - * Purpose: Internal routine to create a new dataset. - * - * Return: Success: Non-NULL, pointer to new dataset object. + * Function: H5D__create_named * - * Failure: NULL + * Purpose: Internal routine to create a new dataset. * - * Programmer: Quincey Koziol - * Thursday, April 5, 2007 + * Return: Success: Non-NULL, pointer to new dataset object. * + * Failure: NULL *------------------------------------------------------------------------- */ H5D_t * H5D__create_named(const H5G_loc_t *loc, const char *name, hid_t type_id, - const H5S_t *space, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id, - hid_t dxpl_id) + const H5S_t *space, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id) { H5O_obj_create_t ocrt_info; /* Information for object creation */ H5D_obj_create_t dcrt_info; /* Information for dataset creation */ - H5D_t *ret_value = NULL; /* Return value */ + H5D_t *ret_value = NULL; /* Return value */ FUNC_ENTER_PACKAGE @@ -472,7 +397,6 @@ H5D__create_named(const H5G_loc_t *loc, const char *name, hid_t type_id, 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; @@ -486,7 +410,7 @@ H5D__create_named(const H5G_loc_t *loc, const char *name, hid_t type_id, 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) + if(H5L_link_object(loc, name, &ocrt_info, lcpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to create and link to dataset") HDassert(ocrt_info.new_obj); @@ -501,25 +425,16 @@ done: /*------------------------------------------------------------------------- * Function: H5D__get_space_status * - * Purpose: Returns the status of data space allocation. + * Purpose: Returns the status of dataspace 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) +H5D__get_space_status(const H5D_t *dset, H5D_space_status_t *allocation) { - 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 @@ -528,6 +443,12 @@ H5D__get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id /* Check for chunked layout */ if(dset->shared->layout.type == H5D_CHUNKED) { + hsize_t space_allocated; /* The number of bytes allocated for chunks */ + hssize_t snelmts; /* Temporary holder for number of elements in dataspace */ + hsize_t nelmts; /* Number of elements in dataspace */ + size_t dt_size; /* Size of datatype */ + hsize_t full_size; /* The number of bytes in the dataset when fully populated */ + /* For chunked layout set the space status by the storage size */ /* Get the dataset's dataspace */ HDassert(dset->shared->space); @@ -549,7 +470,7 @@ H5D__get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id 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) + if(H5D__get_storage_size(dset, &space_allocated) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get size of dataset's storage") /* Decide on how much of the space is allocated */ @@ -557,7 +478,7 @@ H5D__get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED; else if(space_allocated == full_size) *allocation = H5D_SPACE_STATUS_ALLOCATED; - else + else *allocation = H5D_SPACE_STATUS_PART_ALLOCATED; } /* end if */ else { @@ -575,21 +496,16 @@ done: /*------------------------------------------------------------------------- - * Function: H5D__new - * - * Purpose: Creates a new, empty dataset structure - * - * Return: Success: Pointer to a new dataset descriptor. - * - * Failure: NULL + * Function: H5D__new * - * Programmer: Quincey Koziol - * Monday, October 12, 1998 + * Purpose: Creates a new, empty dataset structure * + * Return: Success: Pointer to a new dataset descriptor. + * Failure: NULL *------------------------------------------------------------------------- */ static H5D_shared_t * -H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) +H5D__new(hid_t dcpl_id, hid_t dapl_id, hbool_t creating, hbool_t vl_type) { H5D_shared_t *new_dset = NULL; /* New dataset object */ H5P_genplist_t *plist; /* Property list created */ @@ -602,7 +518,7 @@ H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) 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)); + H5MM_memcpy(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 @@ -620,6 +536,19 @@ H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) new_dset->dcpl_id = H5P_copy_plist(plist, FALSE); } /* end else */ + if(!vl_type && creating && dapl_id == H5P_DATASET_ACCESS_DEFAULT) { + if(H5I_inc_ref(dapl_id, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment default DAPL ID") + new_dset->dapl_id = dapl_id; + } /* end if */ + else { + /* Get the property list */ + if(NULL == (plist = (H5P_genplist_t *)H5I_object(dapl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list") + + new_dset->dapl_id = H5P_copy_plist(plist, FALSE); + } /* end else */ + /* Set return value */ ret_value = new_dset; @@ -628,6 +557,8 @@ done: 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") + if(new_dset->dapl_id != 0 && H5I_dec_ref(new_dset->dapl_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 */ @@ -636,26 +567,22 @@ done: /*------------------------------------------------------------------------- - * Function: H5D__init_type + * Function: H5D__init_type * - * Purpose: Copy a datatype for a dataset's use, performing all the + * 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 - * + * Return: Success: SUCCEED + * Failure: FAIL *------------------------------------------------------------------------- */ static herr_t H5D__init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, const H5T_t *type) { - htri_t relocatable; /* Flag whether the type is relocatable */ - htri_t immutable; /* Flag whether the type is immutable */ - hbool_t use_latest_format; /* Flag indicating the 'latest datatype version support' is enabled */ - herr_t ret_value = SUCCEED; /* Return value */ + htri_t relocatable; /* Flag whether the type is relocatable */ + htri_t immutable; /* Flag whether the type is immutable */ + hbool_t use_at_least_v18; /* Flag indicating to use at least v18 format versions */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -672,32 +599,32 @@ H5D__init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, const H5T_t *type) 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); + /* To use at least v18 format versions or not */ + use_at_least_v18 = (H5F_LOW_BOUND(file) >= H5F_LIBVER_V18); - /* Copy the datatype if it's a custom datatype or if it'll change when it's location is changed */ - if(!immutable || relocatable || use_latest_format) { + /* Copy the datatype if it's a custom datatype or if it'll change when its location is changed */ + if(!immutable || relocatable || use_at_least_v18) { /* Copy datatype for dataset */ if((dset->shared->type = H5T_copy(type, H5T_COPY_ALL)) == NULL) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy datatype") - /* Convert a datatype (if committed) to a transient type if the committed datatype's file - location is different from the file location where the dataset will be created */ + /* 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) + if(H5T_set_loc(dset->shared->type, H5F_VOL_OBJ(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") + /* Set the version for datatype */ + if(H5T_set_version(file, dset->shared->type) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set version of datatype") /* Get a datatype ID for the dataset's datatype */ - if((dset->shared->type_id = H5I_register(H5I_DATATYPE, dset->shared->type, FALSE)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") + 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 { @@ -715,16 +642,12 @@ done: /*------------------------------------------------------------------------- - * Function: H5D__cache_dataspace_info - * - * Purpose: Cache dataspace info for a dataset - * - * Return: Success: SUCCEED - * Failure: FAIL + * Function: H5D__cache_dataspace_info * - * Programmer: Quincey Koziol - * Wednesday, November 19, 2014 + * Purpose: Cache dataspace info for a dataset * + * Return: Success: SUCCEED + * Failure: FAIL *------------------------------------------------------------------------- */ static herr_t @@ -744,7 +667,7 @@ H5D__cache_dataspace_info(const H5D_t *dset) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't cache dataspace dimensions") dset->shared->ndims = (unsigned)sndims; - /* Compute the inital 'power2up' values */ + /* Compute the initial 'power2up' values */ for(u = 0; u < dset->shared->ndims; u++) { hsize_t scaled_power2up; /* Scaled value, rounded to next power of 2 */ @@ -759,23 +682,18 @@ done: /*------------------------------------------------------------------------- - * Function: H5D__init_space + * Function: H5D__init_space * - * Purpose: Copy a dataspace for a dataset's use, performing all the + * 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 - * + * Return: Success: SUCCEED + * Failure: FAIL *------------------------------------------------------------------------- */ 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 @@ -785,9 +703,6 @@ H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space) 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") @@ -796,10 +711,9 @@ H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space) 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 version for dataspace */ + if(H5S_set_version(file, dset->shared->space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype") /* Set the dataset's dataspace to 'all' selection */ if(H5S_select_all(dset->shared->space, TRUE) < 0) @@ -811,31 +725,230 @@ done: /*------------------------------------------------------------------------- - * Function: H5D__update_oh_info + * Function: H5D__use_minimized_dset_headers + * + * Purpose: Compartmentalize check for file- or dcpl-set values indicating + * to create a "minimized" dataset object header. + * Upon success, write resulting value to out pointer `minimize`. + * + * Return: Success: SUCCEED (0) (non-negative value) + * Failure: FAIL (-1) (negative value) + * + * Programmer: Jacob Smith + * 16 August 2018 + *------------------------------------------------------------------------- + */ +static herr_t +H5D__use_minimized_dset_headers(H5F_t *file, hbool_t *minimize) +{ + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(file); + HDassert(minimize); + + /* Get the dataset object header minimize flag for this call */ + if(H5CX_get_dset_min_ohdr_flag(minimize) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset object header minimize flag from API context") + + if(FALSE == *minimize) + *minimize = H5F_get_min_dset_ohdr(file); + +done: + if(FAIL == ret_value) + *minimize = FALSE; + FUNC_LEAVE_NOAPI(ret_value); +} /* H5D__use_minimized_dset_headers */ + + +/*------------------------------------------------------------------------- + * Function: H5D__calculate_minimium_header_size + * + * Purpose: Calculate the size required for the minimized object header. + * + * Return: Success: Positive value > 0 + * Failure: 0 + * + * Programmer: Jacob Smith + * 16 August 2018 + *------------------------------------------------------------------------- + */ +static size_t +H5D__calculate_minimum_header_size(H5F_t *file, H5D_t *dset, H5O_t *ohdr) +{ + H5T_t *type = NULL; + H5O_fill_t *fill_prop = NULL; + hbool_t use_at_least_v18 = FALSE; + const char continuation[1] = ""; /* requred for work-around */ + size_t get_value = 0; + size_t ret_value = 0; + + FUNC_ENTER_STATIC + + HDassert(file); + HDassert(dset); + HDassert(ohdr); + + type = dset->shared->type; + fill_prop = &(dset->shared->dcpl_cache.fill); + use_at_least_v18 = (H5F_LOW_BOUND(file) >= H5F_LIBVER_V18); + + /* Datatype message size */ + get_value = H5O_msg_size_oh(file, ohdr, H5O_DTYPE_ID, type, 0); + if (get_value == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "Can't get size of datatype message") + ret_value += get_value; + + /* Shared Dataspace message size */ + get_value = H5O_msg_size_oh(file, ohdr, H5O_SDSPACE_ID, dset->shared->space, 0); + if (get_value == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of dataspace message") + ret_value += get_value; + + /* "Layout" message size */ + get_value = H5O_msg_size_oh(file, ohdr, H5O_LAYOUT_ID, &dset->shared->layout, 0); + if (get_value == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of layout message") + ret_value += get_value; + + /* Fill Value message size */ + get_value = H5O_msg_size_oh(file, ohdr, H5O_FILL_NEW_ID, fill_prop, 0); + if (get_value == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of fill value message") + ret_value += get_value; + + /* "Continuation" message size */ + /* message pointer "continuation" is unused by raw get function, however, + * a null pointer would be intercepted by an assert in H5O_msg_size_oh(). + */ + get_value = H5O_msg_size_oh(file, ohdr, H5O_CONT_ID, continuation, 0); + if (get_value == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of continuation message") + ret_value += get_value; + + /* Fill Value (backwards compatability) message size */ + if(fill_prop->buf && !use_at_least_v18) { + H5O_fill_t old_fill_prop; /* Copy for writing "old" fill value */ + + /* Shallow copy the fill value property */ + /* guards against shared component modification */ + H5MM_memcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop)); + + if (H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't reset the copied fill property") + + get_value = H5O_msg_size_oh(file, ohdr, H5O_FILL_ID, &old_fill_prop, 0); + if (get_value == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of fill value (backwards compat) message") + ret_value += get_value; + } + + /* Filter/Pipeline message size */ + if(H5D_CHUNKED == dset->shared->layout.type) { + H5O_pline_t *pline = &dset->shared->dcpl_cache.pline; + if(pline->nused > 0) { + get_value = H5O_msg_size_oh(file, ohdr, H5O_PLINE_ID, pline, 0); + if (get_value == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of filter message") + ret_value += get_value; + } + } + + /* External File Link message size */ + if(dset->shared->dcpl_cache.efl.nused > 0) { + get_value = H5O_msg_size_oh(file, ohdr, H5O_EFL_ID, &dset->shared->dcpl_cache.efl, 0); + if (get_value == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of external file link message") + ret_value += get_value; + } + + /* Modification Time message size */ + if(H5O_HDR_STORE_TIMES & H5O_OH_GET_FLAGS(ohdr)) { + HDassert(H5O_OH_GET_VERSION(ohdr) >= 1); /* 1 :: H5O_VERSION_1 (H5Opkg.h) */ + + if(H5O_OH_GET_VERSION(ohdr) == 1) { + /* v1 object headers store modification time as a message */ + time_t mtime; + get_value = H5O_msg_size_oh(file, ohdr, H5O_MTIME_NEW_ID, &mtime, 0); + if (get_value == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of modification time message") + ret_value += get_value; + } + } + +done: + FUNC_LEAVE_NOAPI(ret_value); +} /* H5D__calculate_minimum_header_size */ + + +/*------------------------------------------------------------------------- + * Function: H5D__prepare_minimized_oh * - * Purpose: Create and fill object header for dataset + * Purpose: Create an object header (H5O_t) allocated with the smallest + * possible size. * - * Return: Success: SUCCEED - * Failure: FAIL + * Return: Success: SUCCEED (0) (non-negative value) + * Failure: FAIL (-1) (negative value) * - * Programmer: Bill Wendling - * Thursday, October 31, 2002 + * Programmer: Jacob Smith + * 16 August 2018 + *------------------------------------------------------------------------- + */ +static herr_t +H5D__prepare_minimized_oh(H5F_t *file, H5D_t *dset, H5O_loc_t *oloc) +{ + H5O_t *oh = NULL; + size_t ohdr_size = 0; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_STATIC + + HDassert(file); + HDassert(dset); + HDassert(oloc); + + oh = H5O__create_ohdr(file, dset->shared->dcpl_id); + if(NULL == oh) + HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "can't instantiate object header") + + ohdr_size = H5D__calculate_minimum_header_size(file, dset, oh); + if (ohdr_size == 0) + HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "computed header size is invalid") + + /* Special allocation of space for compact datsets is handled by the call here. */ + if(H5O__apply_ohdr(file, oh, dset->shared->dcpl_id, ohdr_size, (size_t)1, oloc) == FAIL) + HGOTO_ERROR(H5E_OHDR, H5E_BADVALUE, FAIL, "can't apply object header to file") + +done: + FUNC_LEAVE_NOAPI(ret_value); +} /* H5D__prepare_minimized_oh */ + + +/*------------------------------------------------------------------------- + * Function: H5D__update_oh_info + * + * Purpose: Create and fill object header for dataset * + * Return: Success: SUCCEED + * Failure: FAIL *------------------------------------------------------------------------- */ static herr_t -H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id) +H5D__update_oh_info(H5F_t *file, H5D_t *dset, hid_t dapl_id) { - H5O_t *oh = NULL; /* Pointer to dataset's object header */ - size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ - H5O_loc_t *oloc = NULL; /* Dataset's object location */ - H5O_layout_t *layout; /* Dataset's layout information */ - H5T_t *type; /* Dataset's datatype */ - H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ - H5D_fill_value_t fill_status; /* Fill value status */ - hbool_t fill_changed = FALSE; /* Flag indicating the fill value was changed */ - hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */ - herr_t ret_value = SUCCEED; /* Return value */ + H5O_t *oh = NULL; /* Pointer to dataset's object header */ + size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ + H5O_loc_t *oloc = NULL; /* Dataset's object location */ + H5O_layout_t *layout; /* Dataset's layout information */ + H5T_t *type; /* Dataset's datatype */ + H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ + H5D_fill_value_t fill_status; /* Fill value status */ + hbool_t fill_changed = FALSE; /* Flag indicating the fill value was changed */ + hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */ + hbool_t use_at_least_v18; /* Flag indicating to use at least v18 format versions */ + hbool_t use_minimized_header = FALSE; /* Flag to use minimized dataset object headers */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -849,6 +962,9 @@ H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id) type = dset->shared->type; fill_prop = &dset->shared->dcpl_cache.fill; + /* To use at least v18 format versions or not */ + use_at_least_v18 = (H5F_LOW_BOUND(file) >= H5F_LIBVER_V18); + /* Retrieve "defined" status of fill value */ if(H5P_is_fill_value_defined(fill_prop, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") @@ -872,13 +988,14 @@ H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id) /* 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) + if(fill_prop->buf && fill_prop->size > 0 && H5O_fill_convert(fill_prop, type, &fill_changed) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert fill value to dataset type") - fill_prop->fill_defined = TRUE; - } else if(fill_status == H5D_FILL_VALUE_UNDEFINED) { - fill_prop->fill_defined = FALSE; - } else + 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 */ @@ -899,50 +1016,61 @@ H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id) 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; + if(H5D__use_minimized_dset_headers(file, &use_minimized_header) == FAIL) + HGOTO_ERROR(H5E_ARGS, H5E_CANTGET, FAIL, "can't get minimize settings") + + if(TRUE == use_minimized_header) { + if(H5D__prepare_minimized_oh(file, dset, oloc) == FAIL) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't create minimized dataset object header") + } else { + /* Add the dataset's raw data size to the size of the header, if the + * raw data will be stored as compact + */ + if(H5D_COMPACT == layout->type) + ohdr_size += layout->storage.u.compact.size; + + /* Create an object header for the dataset */ + if(H5O_create(file, ohdr_size, (size_t)1, dset->shared->dcpl_id, oloc/*out*/) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header") + } /* if using default/minimized object headers */ - /* 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))) + if(NULL == (oh = H5O_pin(oloc))) HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header") /* Write the dataspace header message */ - if(H5S_append(file, dxpl_id, oh, dset->shared->space) < 0) + if(H5S_append(file, oh, dset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message") /* Write the datatype header message */ - if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0) + if(H5O_msg_append_oh(file, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update datatype header message") /* Write new fill value message */ - if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0) + if(H5O_msg_append_oh(file, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update new fill value header message") /* If there is valid information for the old fill value struct, add it */ - /* (only if we aren't trying to write the 'latest fill message version support') */ - if(fill_prop->buf && !(H5F_USE_LATEST_FLAGS(file, H5F_LATEST_FILL_MSG))) { + /* (only if we aren't using v18 format versions and above */ + if(fill_prop->buf && !use_at_least_v18) { H5O_fill_t old_fill_prop; /* Copy of fill value property, for writing as "old" fill value */ /* Shallow copy the fill value property */ - /* (we only want to make certain that the shared component isnt' modified) */ - HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop)); + /* (we only want to make certain that the shared component isn't modified) */ + H5MM_memcpy(&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) + if(H5O_msg_append_oh(file, oh, H5O_FILL_ID, H5O_MSG_FLAG_CONSTANT, 0, &old_fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update old fill value header message") } /* end if */ /* Update/create the layout (and I/O pipeline & EFL) messages */ - if(H5D__layout_oh_create(file, dxpl_id, oh, dset, dapl_id) < 0) + if(H5D__layout_oh_create(file, oh, dset, dapl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout/pline/efl header message") /* Indicate that the layout information was initialized */ @@ -961,28 +1089,28 @@ H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id) (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 */ + unsigned bogus_id; /* "bogus" ID */ - /* Retrieve "bogus" message 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") + 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) + if(H5O_bogus_oh(file, oh, bogus_id, (unsigned)bogus_flags) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create 'bogus' message") } /* end if */ } #endif /* H5O_ENABLE_BOGUS */ /* Add a modification time message, if using older format. */ - /* (If using the latest 'no modification time message' version support, the modification time is part of the object + /* (If using v18 format versions and above, the the modification time is part of the object * header and doesn't use a separate message -QAK) */ - if(!(H5F_USE_LATEST_FLAGS(file, H5F_LATEST_NO_MOD_TIME_MSG))) - if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0) + if(!use_at_least_v18) + if(H5O_touch_oh(file, oh, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message") done: @@ -995,58 +1123,63 @@ done: 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) + if(dset->shared->layout.ops->dest && (dset->shared->layout.ops->dest)(dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__update_oh_info() */ + /*-------------------------------------------------------------------------- - * Function: H5D_build_extfile_prefix + * Function: H5D__build_file_prefix * - * Purpose: Determine the external file prefix to be used and store - * it in extfile_prefix. Stores an empty string if no prefix + * Purpose: Determine the file prefix to be used and store + * it in file_prefix. Stores an empty string if no prefix * should be used. * * Return: SUCCEED/FAIL - * - * 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*/) +H5D__build_file_prefix(const H5D_t *dset, H5F_prefix_open_t prefix_type, char **file_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 */ + const char *prefix = NULL; /* prefix used to look for the file */ + char *filepath = NULL; /* absolute path of directory the HDF5 file is in */ + size_t filepath_len; /* length of file path */ size_t prefix_len; /* length of prefix */ - size_t extfile_prefix_len; /* length of expanded prefix */ - H5P_genplist_t *plist = NULL; /* Property list pointer */ + size_t file_prefix_len; /* length of expanded prefix */ herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_STATIC + /* Sanity checks */ HDassert(dset); HDassert(dset->oloc.file); - - extpath = H5F_EXTPATH(dset->oloc.file); - HDassert(extpath); + filepath = H5F_EXTPATH(dset->oloc.file); + HDassert(filepath); /* 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 */ + if(H5F_PREFIX_VDS == prefix_type) { + prefix = H5D_prefix_vds_env; + + if(prefix == NULL || *prefix == '\0') { + if(H5CX_get_vds_prefix(&prefix) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get the prefix for vds file") + } + } + else if(H5F_PREFIX_EFILE == prefix_type) { + prefix = H5D_prefix_ext_env; + + if(prefix == NULL || *prefix == '\0') { + if(H5CX_get_ext_file_prefix(&prefix) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get the prefix for the external file") + } + } + else + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "prefix name is not sensible") /* Prefix has to be checked for NULL / empty string again because the * code above might have updated it. @@ -1055,58 +1188,53 @@ H5D_build_extfile_prefix(const H5D_t *dset, hid_t dapl_id, char **extfile_prefix /* 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") + *file_prefix = NULL; } /* end if */ else { - if (HDstrncmp(prefix, "${ORIGIN}", HDstrlen("${ORIGIN}")) == 0) { + if(HDstrncmp(prefix, "${ORIGIN}", HDstrlen("${ORIGIN}")) == 0) { /* Replace ${ORIGIN} at beginning of prefix by directory of HDF5 file */ - extpath_len = HDstrlen(extpath); + filepath_len = HDstrlen(filepath); prefix_len = HDstrlen(prefix); - extfile_prefix_len = extpath_len + prefix_len - HDstrlen("${ORIGIN}") + 1; - - if(NULL == (*extfile_prefix = (char *)H5MM_malloc(extfile_prefix_len))) + file_prefix_len = filepath_len + prefix_len - HDstrlen("${ORIGIN}") + 1; + + if(NULL == (*file_prefix = (char *)H5MM_malloc(file_prefix_len))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate buffer") - HDsnprintf(*extfile_prefix, extfile_prefix_len, "%s%s", extpath, prefix + HDstrlen("${ORIGIN}")); + HDsnprintf(*file_prefix, file_prefix_len, "%s%s", filepath, prefix + HDstrlen("${ORIGIN}")); } /* end if */ else { - if(NULL == (*extfile_prefix = (char *)H5MM_strdup(prefix))) + if(NULL == (*file_prefix = (char *)H5MM_strdup(prefix))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") } /* end else */ } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) -} /* H5D_build_extfile_prefix() */ +} /* H5D__build_file_prefix() */ /*------------------------------------------------------------------------- - * Function: H5D__create - * - * Purpose: Creates a new dataset with name NAME in file F and associates - * with it a datatype TYPE for each element as stored in the - * file, dimensionality information or dataspace SPACE, and - * other miscellaneous properties CREATE_PARMS. All arguments - * are deep-copied before being associated with the new dataset, - * so the caller is free to subsequently modify them without - * affecting the dataset. - * - * Return: Success: Pointer to a new dataset - * - * Failure: NULL - * - * Programmer: Robb Matzke - * Thursday, December 4, 1997 - * + * Function: H5D__create + * + * Purpose: Creates a new dataset with name NAME in file F and associates + * with it a datatype TYPE for each element as stored in the + * file, dimensionality information or dataspace SPACE, and + * other miscellaneous properties CREATE_PARMS. All arguments + * are deep-copied before being associated with the new dataset, + * so the caller is free to subsequently modify them without + * affecting the dataset. + * + * Return: Success: Pointer to a new dataset + * Failure: NULL *------------------------------------------------------------------------- */ H5D_t * H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, - hid_t dapl_id, hid_t dxpl_id) + hid_t dapl_id) { - const H5T_t *type; /* Datatype for dataset */ - H5D_t *new_dset = NULL; - H5P_genplist_t *dc_plist = NULL; /* New Property list */ + H5T_t *type = NULL; /* Datatype for dataset (VOL pointer) */ + H5T_t *dt = NULL; /* Datatype for dataset (non-VOL pointer) */ + 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 */ @@ -1114,7 +1242,7 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, 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 */ + H5D_t *ret_value = NULL; /* Return value */ FUNC_ENTER_PACKAGE @@ -1123,12 +1251,14 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, 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))) + if(NULL == (dt = (H5T_t *)H5I_object(type_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a datatype") + /* If this is a named datatype, get the pointer via the VOL plugin */ + type = H5T_get_actual_type(dt); + /* 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") @@ -1151,7 +1281,7 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, H5G_loc_reset(&dset_loc); /* Initialize the shared dataset space */ - if(NULL == (new_dset->shared = H5D__new(dcpl_id, TRUE, has_vl_type))) + if(NULL == (new_dset->shared = H5D__new(dcpl_id, dapl_id, TRUE, has_vl_type))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") /* Copy & initialize datatype for dataset */ @@ -1213,33 +1343,22 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, /* 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 */ + /* Set the version for the I/O pipeline message */ + if(H5O_pline_set_version(file, &new_dset->shared->dcpl_cache.pline) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of I/O filter pipeline") + + /* Set the version for the fill message */ + if(H5O_fill_set_version(file, &new_dset->shared->dcpl_cache.fill) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of fill value") + + /* Set the latest version for the layout message */ + if(H5D__layout_set_version(file, &new_dset->shared->layout) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of layout") + + if(new_dset->shared->layout.version >= H5O_LAYOUT_VERSION_4) { + /* Use latest indexing type for layout message version >= 4 */ if(H5D__layout_set_latest_indexing(&new_dset->shared->layout, new_dset->shared->space, &new_dset->shared->dcpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest indexing") } /* end if */ @@ -1257,20 +1376,24 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, 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) + if(H5D__update_oh_info(file, new_dset, new_dset->shared->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") + if(H5D__append_flush_setup(new_dset, new_dset->shared->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) + if(H5D__build_file_prefix(new_dset, H5F_PREFIX_EFILE, &new_dset->shared->extfile_prefix) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix") + /* Set the VDS file prefix */ + if(H5D__build_file_prefix(new_dset, H5F_PREFIX_VDS, &new_dset->shared->vds_prefix) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize VDS prefix") + /* Add the dataset to the list of opened objects in the file */ if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count") @@ -1282,10 +1405,10 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, ret_value = new_dset; done: - if(!ret_value && new_dset && new_dset->shared) { + if(!ret_value && new_dset) { 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) + if(new_dset->shared->layout.ops->dest && (new_dset->shared->layout.ops->dest)(new_dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy layout info") if(pline_copied) if(H5O_msg_reset(H5O_PLINE_ID, &new_dset->shared->dcpl_cache.pline) < 0) @@ -1301,21 +1424,34 @@ done: 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(new_dset->shared->type) { + if(new_dset->shared->type_id > 0) { + if(H5I_dec_ref(new_dset->shared->type_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype") + } /* end if */ + else { + if(H5T_close_real(new_dset->shared->type) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype") + } /* end else */ + } /* end if */ + if(H5F_addr_defined(new_dset->oloc.addr)) { - if(H5O_dec_rc_by_loc(&(new_dset->oloc), dxpl_id) < 0) + if(H5O_dec_rc_by_loc(&(new_dset->oloc)) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement refcount on newly created object") if(H5O_close(&(new_dset->oloc), NULL) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header") if(file) { - if(H5O_delete(file, dxpl_id, new_dset->oloc.addr) < 0) + if(H5O_delete(file, new_dset->oloc.addr) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDELETE, NULL, "unable to delete object header") } /* end if */ } /* end if */ if(new_dset->shared->dcpl_id != 0 && H5I_dec_ref(new_dset->shared->dcpl_id) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list") + if(new_dset->shared->dapl_id != 0 && H5I_dec_ref(new_dset->shared->dapl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list") new_dset->shared->extfile_prefix = (char *)H5MM_xfree(new_dset->shared->extfile_prefix); + new_dset->shared->vds_prefix = (char *)H5MM_xfree(new_dset->shared->vds_prefix); new_dset->shared = H5FL_FREE(H5D_shared_t, new_dset->shared); } /* end if */ new_dset->oloc.file = NULL; @@ -1333,15 +1469,10 @@ done: * * 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__open_name(const H5G_loc_t *loc, const char *name, hid_t dapl_id) { H5D_t *dset = NULL; H5G_loc_t dset_loc; /* Object location of dataset */ @@ -1363,18 +1494,18 @@ H5D__open_name(const H5G_loc_t *loc, const char *name, hid_t dapl_id, H5G_loc_reset(&dset_loc); /* Find the dataset object */ - if(H5G_loc_find(loc, name, &dset_loc, dapl_id, dxpl_id) < 0) + if(H5G_loc_find(loc, name, &dset_loc) < 0) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found") loc_found = TRUE; /* Check that the object found is the correct type */ - if(H5O_obj_type(&oloc, &obj_type, dxpl_id) < 0) + if(H5O_obj_type(&oloc, &obj_type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "can't get object type") if(obj_type != H5O_TYPE_DATASET) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, NULL, "not a dataset") /* Open the dataset */ - if(NULL == (dset = H5D_open(&dset_loc, dapl_id, dxpl_id))) + if(NULL == (dset = H5D_open(&dset_loc, dapl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't open dataset") /* Set return value */ @@ -1391,25 +1522,22 @@ done: /* *------------------------------------------------------------------------- - * Function: H5D_open + * Function: H5D_open * - * Purpose: Checks if dataset is already open, or opens a dataset for + * 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 - * + * Return: Success: Dataset ID + * Failure: FAIL *------------------------------------------------------------------------- */ H5D_t * -H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id) +H5D_open(const H5G_loc_t *loc, hid_t dapl_id) { H5D_shared_t *shared_fo = NULL; H5D_t *dataset = NULL; char *extfile_prefix = NULL; /* Expanded external file prefix */ + char *vds_prefix = NULL; /* Expanded vds prefix */ H5D_t *ret_value = NULL; /* Return value */ FUNC_ENTER_NOAPI(NULL) @@ -1422,7 +1550,7 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id) 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) + if(H5O_loc_copy_shallow(&(dataset->oloc), loc->oloc) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy object location") /* Shallow copy (take ownership) of the group hier. path */ @@ -1430,16 +1558,20 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id) 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) + if(H5D__build_file_prefix(dataset, H5F_PREFIX_EFILE, &extfile_prefix) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix") + /* Get the VDS prefix */ + if(H5D__build_file_prefix(dataset, H5F_PREFIX_VDS, &vds_prefix) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize VDS prefix") + /* Check if dataset was already open */ if(NULL == (shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr))) { /* Clear any errors from H5FO_opened() */ H5E_clear_stack(NULL); /* Open the dataset object */ - if(H5D__open_oid(dataset, dapl_id, dxpl_id) < 0) + if(H5D__open_oid(dataset, dapl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found") /* Add the dataset to the list of opened objects in the file */ @@ -1458,6 +1590,11 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id) /* Prevent string from being freed during done: */ extfile_prefix = NULL; + /* Set the vds file prefix */ + dataset->shared->vds_prefix = vds_prefix; + /* Prevent string from being freed during done: */ + vds_prefix = NULL; + } /* end if */ else { /* Point to shared info */ @@ -1469,8 +1606,13 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id) /* 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") + if(extfile_prefix && dataset->shared->extfile_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") + } else { + if(extfile_prefix || dataset->shared->extfile_prefix) + 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) { @@ -1489,12 +1631,14 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id) done: extfile_prefix = (char *)H5MM_xfree(extfile_prefix); + vds_prefix = (char *)H5MM_xfree(vds_prefix); if(ret_value == NULL) { /* Free the location--casting away const*/ if(dataset) { if(shared_fo == NULL && dataset->shared) { /* Need to free shared fo */ dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix); + dataset->shared->vds_prefix = (char *)H5MM_xfree(dataset->shared->vds_prefix); dataset->shared = H5FL_FREE(H5D_shared_t, dataset->shared); } @@ -1513,19 +1657,15 @@ done: /* *------------------------------------------------------------------------- - * Function: H5D__flush_append_setup - * - * Purpose: Set the append flush parameters for a dataset + * Function: H5D__flush_append_setup * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Vailin Choi - * Wednesday, January 8, 2014 + * Purpose: Set the append flush parameters for a dataset * + * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ static herr_t -H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id) +H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id) { herr_t ret_value = SUCCEED; /* return value */ @@ -1542,47 +1682,47 @@ H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id) 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"); + /* 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) { + /* 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; + /* 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") + 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 */ + dset->shared->append_flush.ndims = info.ndims; + dset->shared->append_flush.func = info.func; + dset->shared->append_flush.udata = info.udata; + H5MM_memcpy(dset->shared->append_flush.boundary, info.boundary, sizeof(info.boundary)); + } /* end if */ + } /* end if */ } /* end if */ done: @@ -1591,34 +1731,30 @@ done: /*------------------------------------------------------------------------- - * Function: H5D__open_oid + * 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 + * Purpose: Opens a dataset for access. * + * Return: Dataset pointer on success, NULL on failure *------------------------------------------------------------------------- */ static herr_t -H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id) +H5D__open_oid(H5D_t *dataset, hid_t dapl_id) { H5P_genplist_t *plist; /* Property list */ H5O_fill_t *fill_prop; /* Pointer to dataset's fill value info */ unsigned alloc_time_state; /* Allocation time state */ htri_t msg_exists; /* Whether a particular type of message exists */ - hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */ - herr_t ret_value = SUCCEED; /* Return value */ + 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) + FUNC_ENTER_STATIC_TAG(dataset->oloc.addr) /* check args */ HDassert(dataset); /* (Set the 'vl_type' parameter to FALSE since it doesn't matter from here) */ - if(NULL == (dataset->shared = H5D__new(H5P_DATASET_CREATE_DEFAULT, FALSE, FALSE))) + if(NULL == (dataset->shared = H5D__new(H5P_DATASET_CREATE_DEFAULT, dapl_id, FALSE, FALSE))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") /* Open the dataset object */ @@ -1626,13 +1762,13 @@ H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id) 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))) + if(NULL == (dataset->shared->type = (H5T_t *)H5O_msg_read(&(dataset->oloc), H5O_DTYPE_ID, NULL))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load type info from dataset header") - if(H5T_set_loc(dataset->shared->type, dataset->oloc.file, H5T_LOC_DISK) < 0) + if(H5T_set_loc(dataset->shared->type, H5F_VOL_OBJ(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))) + if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header") /* Cache the dataset's dataspace info */ @@ -1648,7 +1784,7 @@ H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_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) + if(H5D__layout_oh_read(dataset, dapl_id, plist) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get layout/pline/efl info") /* Indicate that the layout information was initialized */ @@ -1656,24 +1792,24 @@ H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id) /* 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") + 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) + if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_FILL_NEW_ID)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists") if(msg_exists) { - if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_NEW_ID, fill_prop, dxpl_id)) + if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_NEW_ID, fill_prop)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message") } /* end if */ else { - /* For backward compatibility, try to retrieve the old fill value message */ - if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_FILL_ID, dxpl_id)) < 0) + /* For backward compatibility, try to retrieve the old fill value message */ + if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_FILL_ID)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists") if(msg_exists) { - if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_ID, fill_prop, dxpl_id)) + if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_ID, fill_prop)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message") } /* end if */ else { @@ -1732,8 +1868,6 @@ H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id) 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") @@ -1744,8 +1878,8 @@ done: 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) + if(layout_init) + if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") if(dataset->shared->space && H5S_close(dataset->shared->space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") @@ -1755,29 +1889,25 @@ done: HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") } /* end if */ else { - if(H5T_close(dataset->shared->type) < 0) + if(H5T_close_real(dataset->shared->type) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") } /* end else */ } /* end if */ } /* end if */ } /* end if */ - FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL) + FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__open_oid() */ /*------------------------------------------------------------------------- - * Function: H5D_close - * - * Purpose: Insures that all data has been saved to the file, closes the - * dataset object header, and frees all resources used by the - * descriptor. - * - * Return: Non-negative on success/Negative on failure + * Function: H5D_close * - * Programmer: Robb Matzke - * Thursday, December 4, 1997 + * Purpose: Insures that all data has been saved to the file, closes the + * dataset object header, and frees all resources used by the + * descriptor. * + * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ herr_t @@ -1803,7 +1933,7 @@ H5D_close(H5D_t *dataset) 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) + if(H5D__flush_real(dataset) < 0) HDONE_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to flush cached dataset info") /* Set a flag to indicate the dataset is closing, before we start freeing things */ @@ -1883,12 +2013,15 @@ H5D_close(H5D_t *dataset) } /* 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) + if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") /* Free the external file prefix */ dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix); + /* Free the vds file prefix */ + dataset->shared->vds_prefix = (char *)H5MM_xfree(dataset->shared->vds_prefix); + /* Release layout, fill-value, efl & pipeline messages */ if(dataset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT) free_failed |= (H5O_msg_reset(H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline) < 0) || @@ -1900,34 +2033,34 @@ H5D_close(H5D_t *dataset) 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) + 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 + /* Release datatype, dataspace, and creation and access property lists -- 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); + (H5I_dec_ref(dataset->shared->dcpl_id) < 0) || + (H5I_dec_ref(dataset->shared->dapl_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") + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") + if(H5FO_delete(dataset->oloc.file, dataset->oloc.addr) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't remove dataset from list of open objects") /* Close the dataset object */ /* (This closes the file, if this is the last object open) */ if(H5O_close(&(dataset->oloc), &file_closed) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") /* Evict dataset metadata if evicting on close */ if(!file_closed && H5F_SHARED(dataset->oloc.file) && H5F_EVICT_ON_CLOSE(dataset->oloc.file)) { - if(H5AC_flush_tagged_metadata(dataset->oloc.file, dataset->oloc.addr, 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") + if(H5AC_flush_tagged_metadata(dataset->oloc.file, dataset->oloc.addr) < 0) + HDONE_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush tagged metadata") + if(H5AC_evict_tagged_metadata(dataset->oloc.file, dataset->oloc.addr, FALSE) < 0) + HDONE_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to evict tagged metadata") } /* end if */ /* @@ -1973,31 +2106,29 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_mult_refresh_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 + * Purpose: Closing down the needed information when the dataset has + * multiple opens. (From H5O__refresh_metadata_close()) * + * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ herr_t -H5D_mult_refresh_close(hid_t dset_id, hid_t dxpl_id) +H5D_mult_refresh_close(hid_t dset_id) { - H5D_t *dataset; /* Dataset to refresh */ - herr_t ret_value = SUCCEED; /* return value */ + 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))) + if(NULL == (dataset = (H5D_t *)H5VL_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); + HDassert(dataset->oloc.file); + HDassert(dataset->shared); HDassert(dataset->shared->fo_count > 0); if(dataset->shared->fo_count > 1) { @@ -2045,7 +2176,7 @@ H5D_mult_refresh_close(hid_t dset_id, hid_t dxpl_id) } /* 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) + if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info") } /* end if */ @@ -2055,20 +2186,16 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_mult_refresh_reopen - * - * Purpose: Re-initialize the needed info when the dataset has multiple - * opens. (From H5O_refresh_metadata_reopen()) + * Function: H5D_mult_refresh_reopen * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Vailin Choi - * 12/24/15 + * Purpose: Re-initialize the needed info when the dataset has multiple + * opens. * + * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ herr_t -H5D_mult_refresh_reopen(H5D_t *dataset, hid_t dxpl_id) +H5D_mult_refresh_reopen(H5D_t *dataset) { herr_t ret_value = SUCCEED; /* Return value */ @@ -2079,25 +2206,25 @@ H5D_mult_refresh_reopen(H5D_t *dataset, hid_t dxpl_id) 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") + /* Release dataspace info */ + if(H5S_close(dataset->shared->space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + + /* Re-load dataspace info */ + if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load dataspace info from dataset header") + + /* Cache the dataset's dataspace info */ + if(H5D__cache_dataspace_info(dataset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't cache dataspace info") + + /* Release layout info */ + if(H5O_msg_reset(H5O_LAYOUT_ID, &dataset->shared->layout) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRESET, FAIL, "unable to reset layout info") + + /* Re-load layout message info */ + if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message") } /* end if */ done: @@ -2106,16 +2233,12 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_oloc - * - * Purpose: Returns a pointer to the object location for a dataset. - * - * Return: Success: Ptr to location - * Failure: NULL + * Function: H5D_oloc * - * Programmer: Robb Matzke - * Friday, April 24, 1998 + * Purpose: Returns a pointer to the object location for a dataset. * + * Return: Success: Ptr to location + * Failure: NULL *------------------------------------------------------------------------- */ H5O_loc_t * @@ -2129,66 +2252,30 @@ H5D_oloc(H5D_t *dataset) /*------------------------------------------------------------------------- - * Function: H5D_nameof + * 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 + * Purpose: Returns a pointer to the group hier. path for a dataset. * + * Return: Success: Ptr to entry + * Failure: NULL *------------------------------------------------------------------------- */ H5G_name_t * -H5D_nameof(H5D_t *dataset) +H5D_nameof(const 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) + FUNC_LEAVE_NOAPI(dataset ? &(dataset->path) : NULL) } /* end H5D_nameof() */ /*------------------------------------------------------------------------- - * Function: H5D_typeof - * - * Purpose: Returns a pointer to the dataset's datatype. The datatype - * is not copied. + * Function: H5D__alloc_storage * - * 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 + * Purpose: Allocate storage for the raw data of a dataset. * + * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ herr_t @@ -2196,11 +2283,11 @@ 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 */ + 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 @@ -2212,7 +2299,7 @@ H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, * 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)) { + if(!(0 == H5S_GET_EXTENT_NPOINTS(dset->shared->space) || dset->shared->dcpl_cache.efl.nused > 0)) { /* Get a pointer to the dataset's layout information */ layout = &(dset->shared->layout); @@ -2222,7 +2309,7 @@ H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, /* 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) + if(H5D__contig_alloc(f, &layout->storage.u.contig/*out*/) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage") /* Indicate that we should initialize storage space */ @@ -2239,7 +2326,7 @@ H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, 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) + if(H5D__chunk_create(dset /*in,out*/) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") /* Indicate that we set the storage addr */ @@ -2250,19 +2337,18 @@ H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, } /* end if */ /* If space allocation is set to 'early' and we are extending - * the dataset, indicate that space should be allocated, so the + * 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; + 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 + /* 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) { @@ -2274,7 +2360,8 @@ H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, /* Indicate that we should initialize storage space */ must_init_space = TRUE; - } else { + } + else { layout->storage.u.compact.dirty = FALSE; must_init_space = FALSE; } @@ -2316,7 +2403,7 @@ H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, 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 */ + 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) @@ -2340,7 +2427,7 @@ H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, */ 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) + if(H5D__mark(dset, H5D_MARK_LAYOUT) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to mark dataspace as dirty") } /* end if */ @@ -2350,24 +2437,20 @@ done: /*------------------------------------------------------------------------- - * 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. + * Function: H5D__init_storage * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Monday, October 5, 1998 + * Purpose: Initialize the data for a new dataset. If a selection is + * defined for SPACE then initialize only that part of the + * dataset. * + * Return: Non-negative on success/Negative on failure *------------------------------------------------------------------------- */ static herr_t H5D__init_storage(const H5D_io_info_t *io_info, hbool_t full_overwrite, hsize_t old_dim[]) { const H5D_t *dset = io_info->dset; /* dataset pointer */ - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -2378,7 +2461,7 @@ H5D__init_storage(const H5D_io_info_t *io_info, hbool_t full_overwrite, hsize_t /* 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) + if(H5D__compact_fill(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize compact dataset storage") } /* end if */ break; @@ -2426,29 +2509,25 @@ done: /*------------------------------------------------------------------------- - * Function: H5D__get_storage_size - * - * Purpose: Determines how much space has been reserved to store the raw - * data of a dataset. + * Function: H5D__get_storage_size * - * Return: Non-negative on success, negative on failure - * - * Programmer: Robb Matzke - * Wednesday, April 21, 1999 + * Purpose: Determines how much space has been reserved to store the raw + * data of a dataset. * + * Return: Non-negative on success, negative on failure *------------------------------------------------------------------------- */ herr_t -H5D__get_storage_size(H5D_t *dset, hid_t dxpl_id, hsize_t *storage_size) +H5D__get_storage_size(const H5D_t *dset, hsize_t *storage_size) { - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_PACKAGE_TAG(dxpl_id, dset->oloc.addr, FAIL) + FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) switch(dset->shared->layout.type) { case H5D_CHUNKED: if((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) { - if(H5D__chunk_allocated(dset, dxpl_id, storage_size) < 0) + if(H5D__chunk_allocated(dset, storage_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve chunked dataset allocated size") } /* end if */ else @@ -2480,29 +2559,26 @@ H5D__get_storage_size(H5D_t *dset, hid_t dxpl_id, hsize_t *storage_size) } /*lint !e788 All appropriate cases are covered */ done: - FUNC_LEAVE_NOAPI_TAG(ret_value, 0) + FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__get_storage_size() */ /*------------------------------------------------------------------------- - * Function: H5D__get_offset + * Function: H5D__get_offset * - * Purpose: Private function for H5D__get_offset. Returns the address + * Purpose: Private function for H5Dget_offset(). Returns the address * of dataset in file. * - * Return: Success: the address of dataset - * - * Failure: HADDR_UNDEF + * Return: Success: The address of dataset * - * Programmer: Raymond Lu - * November 6, 2002 + * Failure: HADDR_UNDEF (but also a valid value) * *------------------------------------------------------------------------- */ haddr_t H5D__get_offset(const H5D_t *dset) { - haddr_t ret_value = HADDR_UNDEF; + haddr_t ret_value = HADDR_UNDEF; FUNC_ENTER_PACKAGE @@ -2516,7 +2592,8 @@ H5D__get_offset(const H5D_t *dset) case H5D_CONTIGUOUS: /* If dataspace hasn't been allocated or dataset is stored in - * an external file, the value will be HADDR_UNDEF. */ + * 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); @@ -2526,7 +2603,7 @@ H5D__get_offset(const H5D_t *dset) 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) @@ -2534,99 +2611,87 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_vlen_reclaim + * Function: H5D__vlen_get_buf_size_alloc * - * 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. + * 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, November 22, 2005 + * Return: Non-negative on success, negative on failure * *------------------------------------------------------------------------- */ -herr_t -H5D_vlen_reclaim(hid_t type_id, H5S_t *space, hid_t plist_id, void *buf) +static void * +H5D__vlen_get_buf_size_alloc(size_t size, void *info) { - 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); + H5D_vlen_bufsize_common_t *vlen_bufsize_com = (H5D_vlen_bufsize_common_t *)info; + void *ret_value = NULL; /* Return value */ - if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype") + FUNC_ENTER_STATIC - /* 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") + /* Check for increasing the size of the temporary space for VL data */ + if(size > vlen_bufsize_com->vl_tbuf_size) { + if(NULL == (vlen_bufsize_com->vl_tbuf = H5FL_BLK_REALLOC(vlen_vl_buf, vlen_bufsize_com->vl_tbuf, size))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't reallocate temporary VL data buffer") + vlen_bufsize_com->vl_tbuf_size = size; + } /* end if */ - /* 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; + /* Increment size of VL data buffer needed */ + vlen_bufsize_com->size += size; - ret_value = H5S_select_iterate(buf, type, space, &dset_op, vl_alloc_info); + /* Set return value */ + ret_value = vlen_bufsize_com->vl_tbuf; done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_vlen_reclaim() */ +} /* end H5D__vlen_get_buf_size_alloc() */ /*------------------------------------------------------------------------- - * 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. + * Function: H5D__vlen_get_buf_size_cb * - * Return: Non-negative on success, negative on failure + * Purpose: Dataspace selection iteration callback for H5Dvlen_get_buf_size. * - * Programmer: Quincey Koziol - * Tuesday, August 17, 1999 + * Return: Non-negative on success, negative on failure * *------------------------------------------------------------------------- */ -void * -H5D__vlen_get_buf_size_alloc(size_t size, void *info) +static herr_t +H5D__vlen_get_buf_size_cb(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 *)info; - void *ret_value = NULL; /* Return value */ + H5D_vlen_bufsize_native_t *vlen_bufsize = (H5D_vlen_bufsize_native_t *)op_data; + herr_t ret_value = H5_ITER_CONT; /* Return value */ - FUNC_ENTER_PACKAGE_NOERR + FUNC_ENTER_STATIC + + /* Sanity check */ + HDassert(H5I_DATATYPE == H5I_get_type(type_id)); + HDassert(point); + HDassert(op_data); - /* 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; + /* 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, H5_ITER_ERROR, "can't select point") - /* Set return value */ - ret_value = vlen_bufsize->vl_tbuf; + /* 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->common.fl_tbuf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "can't read point") +done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__vlen_get_buf_size_alloc() */ +} /* end H5D__vlen_get_buf_size_cb() */ /*------------------------------------------------------------------------- - * Function: H5D__vlen_get_buf_size + * 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. + * Purpose: This routine checks the number of bytes required to store the VL + * data from the dataset, using the space_id for the selection in the + * dataset on disk and the type_id for the memory representation of the + * VL data, in memory. The *size value is modified according to how many + * bytes are required to store the VL data in memory. * * Implementation: This routine actually performs the read with a custom * memory manager which basically just counts the bytes requested and @@ -2636,31 +2701,129 @@ H5D__vlen_get_buf_size_alloc(size_t size, void *info) * 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 + * Return: Non-negative on success, negative on failure * - * Programmer: Quincey Koziol - * Tuesday, August 17, 1999 + * Programmer: Quincey Koziol + * Wednesday, August 11, 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_get_buf_size(H5D_t *dset, hid_t type_id, hid_t space_id, + hsize_t *size) { - H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)op_data; + H5D_vlen_bufsize_native_t vlen_bufsize = {NULL, NULL, NULL, {NULL, NULL, 0, 0}}; + H5S_t *fspace = NULL; /* Dataset's dataspace */ + H5S_t *mspace = NULL; /* Memory dataspace */ + char bogus; /* bogus value to pass to H5Diterate() */ + H5S_t *space; /* Dataspace for iteration */ + H5T_t *type; /* Datatype */ + H5S_sel_iter_op_t dset_op; /* Operator for iteration */ + herr_t ret_value = FAIL; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check args */ + if(NULL == (type = (H5T_t *)H5I_object(type_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype") + if(NULL == (space = (H5S_t *)H5I_object(space_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace") + if(!(H5S_has_extent(space))) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspace does not have extent set") + + /* Save the dataset */ + vlen_bufsize.dset = dset; + + /* Get a copy of the dataset's dataspace */ + if(NULL == (fspace = H5S_copy(dset->shared->space, FALSE, TRUE))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to get dataspace") + vlen_bufsize.fspace = fspace; + + /* Create a scalar for the memory dataspace */ + if(NULL == (mspace = H5S_create(H5S_SCALAR))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create dataspace") + vlen_bufsize.mspace = mspace; + + /* Grab the temporary buffers required */ + if(NULL == (vlen_bufsize.common.fl_tbuf = H5FL_BLK_MALLOC(vlen_fl_buf, H5T_get_size(type)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available") + if(NULL == (vlen_bufsize.common.vl_tbuf = H5FL_BLK_MALLOC(vlen_vl_buf, (size_t)1))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available") + vlen_bufsize.common.vl_tbuf_size = 1; + + /* Set the memory manager to the special allocation routine */ + if(H5CX_set_vlen_alloc_info(H5D__vlen_get_buf_size_alloc, &vlen_bufsize.common, NULL, NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set VL data allocation routine") + + /* Set the initial number of bytes required */ + vlen_bufsize.common.size = 0; + + /* Call H5S_select_iterate with args, etc. */ + dset_op.op_type = H5S_SEL_ITER_OP_APP; + dset_op.u.app_op.op = H5D__vlen_get_buf_size_cb; + dset_op.u.app_op.type_id = type_id; + + ret_value = H5S_select_iterate(&bogus, type, space, &dset_op, &vlen_bufsize); + + /* Get the size if we succeeded */ + if(ret_value >= 0) + *size = vlen_bufsize.common.size; + +done: + if(fspace && H5S_close(fspace) < 0) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + if(mspace && H5S_close(mspace) < 0) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + if(vlen_bufsize.common.fl_tbuf != NULL) + vlen_bufsize.common.fl_tbuf = H5FL_BLK_FREE(vlen_fl_buf, vlen_bufsize.common.fl_tbuf); + if(vlen_bufsize.common.vl_tbuf != NULL) + vlen_bufsize.common.vl_tbuf = H5FL_BLK_FREE(vlen_vl_buf, vlen_bufsize.common.vl_tbuf); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__vlen_get_buf_size() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__vlen_get_buf_size_gen_cb + * + * 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 + *------------------------------------------------------------------------- + */ +static herr_t +H5D__vlen_get_buf_size_gen_cb(void H5_ATTR_UNUSED *elem, hid_t type_id, + unsigned H5_ATTR_UNUSED ndim, const hsize_t *point, void *op_data) +{ + H5D_vlen_bufsize_generic_t *vlen_bufsize = (H5D_vlen_bufsize_generic_t *)op_data; H5T_t *dt; /* Datatype for operation */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_PACKAGE + FUNC_ENTER_STATIC + /* Sanity check */ + HDassert(point); 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)))) + if(NULL == (vlen_bufsize->common.fl_tbuf = H5FL_BLK_REALLOC(vlen_fl_buf, vlen_bufsize->common.fl_tbuf, H5T_get_size(dt)))) HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, FAIL, "can't resize tbuf") /* Select point to read in */ @@ -2668,27 +2831,136 @@ H5D__vlen_get_buf_size(void H5_ATTR_UNUSED *elem, hid_t type_id, unsigned H5_ATT 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) + if(H5VL_dataset_read(vlen_bufsize->dset_vol_obj, type_id, vlen_bufsize->mspace_id, vlen_bufsize->fspace_id, vlen_bufsize->dxpl_id, vlen_bufsize->common.fl_tbuf, H5_REQUEST_NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point") done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__vlen_get_buf_size() */ +} /* end H5D__vlen_get_buf_size_gen_cb() */ /*------------------------------------------------------------------------- - * Function: H5D__check_filters + * Function: H5D__vlen_get_buf_size_gen * - * Purpose: Check if the filters have be initialized for the dataset + * Purpose: Generic routine to checks the number of bytes required to store the + * VL data from the dataset. * - * Return: Non-negative on success/Negative on failure + * Return: Non-negative on success, negative on failure * - * Programmer: Quincey Koziol - * Thursday, October 11, 2007 + * Programmer: Quincey Koziol + * Friday, December 20, 2019 * *------------------------------------------------------------------------- */ herr_t +H5D__vlen_get_buf_size_gen(H5VL_object_t *vol_obj, hid_t type_id, hid_t space_id, + hsize_t *size) +{ + H5D_vlen_bufsize_generic_t vlen_bufsize = {NULL, H5I_INVALID_HID, NULL, H5I_INVALID_HID, H5I_INVALID_HID, {NULL, NULL, 0, 0}}; + H5P_genplist_t *dxpl = NULL; /* DXPL for operation */ + H5S_t *mspace = NULL; /* Memory dataspace */ + char bogus; /* Bogus value to pass to H5Diterate() */ + H5S_t *space; /* Dataspace for iteration */ + H5T_t *type; /* Datatype */ + H5S_sel_iter_op_t dset_op; /* Operator for iteration */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check args */ + if(NULL == (type = (H5T_t *)H5I_object(type_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not an valid datatype") + if(NULL == (space = (H5S_t *)H5I_object(space_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "invalid dataspace") + if(!(H5S_has_extent(space))) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "dataspace does not have extent set") + + /* Save the dataset */ + vlen_bufsize.dset_vol_obj = vol_obj; + + /* Get a copy of the dataset's dataspace */ + if(H5VL_dataset_get(vol_obj, H5VL_DATASET_GET_SPACE, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, &vlen_bufsize.fspace_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace") + if(NULL == (vlen_bufsize.fspace = (H5S_t *)H5I_object(vlen_bufsize.fspace_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not a dataspace") + + /* Create a scalar for the memory dataspace */ + if(NULL == (mspace = H5S_create(H5S_SCALAR))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create dataspace") + if((vlen_bufsize.mspace_id = H5I_register(H5I_DATASPACE, mspace, TRUE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID") + + /* Grab the temporary buffers required */ + if(NULL == (vlen_bufsize.common.fl_tbuf = H5FL_BLK_MALLOC(vlen_fl_buf, H5T_get_size(type)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "no temporary buffers available") + if(NULL == (vlen_bufsize.common.vl_tbuf = H5FL_BLK_MALLOC(vlen_vl_buf, (size_t)1))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "no temporary buffers available") + vlen_bufsize.common.vl_tbuf_size = 1; + + /* Set the VL allocation callbacks on a DXPL */ + if(NULL == (dxpl = (H5P_genplist_t *)H5I_object(H5P_DATASET_XFER_DEFAULT))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get default DXPL") + if((vlen_bufsize.dxpl_id = H5P_copy_plist(dxpl, TRUE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy property list"); + if(NULL == (dxpl = (H5P_genplist_t *)H5I_object(vlen_bufsize.dxpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get copied DXPL") + if(H5P_set_vlen_mem_manager(dxpl, H5D__vlen_get_buf_size_alloc, &vlen_bufsize.common, NULL, NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set VL data allocation routine on DXPL") + + /* Set the initial number of bytes required */ + vlen_bufsize.common.size = 0; + + /* Call H5S_select_iterate with args, etc. */ + dset_op.op_type = H5S_SEL_ITER_OP_APP; + dset_op.u.app_op.op = H5D__vlen_get_buf_size_gen_cb; + dset_op.u.app_op.type_id = type_id; + + ret_value = H5S_select_iterate(&bogus, type, space, &dset_op, &vlen_bufsize); + + /* Get the size if we succeeded */ + if(ret_value >= 0) + *size = vlen_bufsize.common.size; + +done: + if(vlen_bufsize.fspace_id >= 0) { + if(H5I_dec_app_ref(vlen_bufsize.fspace_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "problem freeing id") + vlen_bufsize.fspace = NULL; + } /* end if */ + if(vlen_bufsize.fspace && H5S_close(vlen_bufsize.fspace) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + if(vlen_bufsize.mspace_id >= 0) { + if(H5I_dec_app_ref(vlen_bufsize.mspace_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "problem freeing id") + mspace = NULL; + } /* end if */ + if(mspace && H5S_close(mspace) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + if(vlen_bufsize.common.fl_tbuf != NULL) + vlen_bufsize.common.fl_tbuf = H5FL_BLK_FREE(vlen_fl_buf, vlen_bufsize.common.fl_tbuf); + if(vlen_bufsize.common.vl_tbuf != NULL) + vlen_bufsize.common.vl_tbuf = H5FL_BLK_FREE(vlen_vl_buf, vlen_bufsize.common.vl_tbuf); + if(vlen_bufsize.dxpl_id != H5I_INVALID_HID) { + if(H5I_dec_app_ref(vlen_bufsize.dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't close property list") + dxpl = NULL; + } /* end if */ + if(dxpl && H5P_close(dxpl) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release DXPL") + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__vlen_get_buf_size_gen() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__check_filters + * + * Purpose: Check if the filters have be initialized for the dataset + * + * Return: Non-negative on success/Negative on failure + *------------------------------------------------------------------------- + */ +herr_t H5D__check_filters(H5D_t *dataset) { H5O_fill_t *fill; /* Dataset's fill value */ @@ -2731,27 +3003,24 @@ done: /*------------------------------------------------------------------------- - * 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 + * Function: H5D__set_extent * - * Return: Non-negative on success, negative on failure - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * April 9, 2002 + * Purpose: Based on H5D_extend, allows change to a lower dimension, + * calls H5S_set_extent and H5D__chunk_prune_by_extent instead * + * Return: Non-negative on success, negative on failure *------------------------------------------------------------------------- */ herr_t -H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) +H5D__set_extent(H5D_t *dset, const hsize_t *size) { hsize_t curr_dims[H5S_MAX_RANK]; /* Current dimension sizes */ htri_t changed; /* Whether the dataspace changed size */ size_t u, v; /* Local index variable */ + unsigned dim_idx; /* Dimension index */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_PACKAGE_TAG(dxpl_id, dset->oloc.addr, FAIL) + FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) /* Check args */ HDassert(dset); @@ -2773,7 +3042,7 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) /* 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])); + H5MM_memcpy(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) @@ -2786,11 +3055,11 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) 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++) { + for(dim_idx = 0; dim_idx < dset->shared->ndims; dim_idx++) { /* Check for various status changes */ - if(size[u] < curr_dims[u]) + if(size[dim_idx] < curr_dims[dim_idx]) shrink = TRUE; - if(size[u] > curr_dims[u]) + if(size[dim_idx] > curr_dims[dim_idx]) expand = TRUE; /* Chunked storage specific checks */ @@ -2798,30 +3067,33 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) hsize_t scaled; /* Scaled value */ /* Compute the scaled dimension size value */ - scaled = size[u] / dset->shared->layout.u.chunk.dim[u]; + if(dset->shared->layout.u.chunk.dim[dim_idx] == 0) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", dim_idx) + + scaled = size[dim_idx] / dset->shared->layout.u.chunk.dim[dim_idx]; /* Check if scaled dimension size changed */ - if(scaled != dset->shared->cache.chunk.scaled_dims[u]) { + if(scaled != dset->shared->cache.chunk.scaled_dims[dim_idx]) { hsize_t scaled_power2up; /* Scaled value, rounded to next power of 2 */ /* Update the scaled dimension size value for the current dimension */ - dset->shared->cache.chunk.scaled_dims[u] = scaled; + dset->shared->cache.chunk.scaled_dims[dim_idx] = scaled; /* Check if algorithm for computing hash values will change */ if((scaled > dset->shared->cache.chunk.nslots && - dset->shared->cache.chunk.scaled_dims[u] <= dset->shared->cache.chunk.nslots) + dset->shared->cache.chunk.scaled_dims[dim_idx] <= dset->shared->cache.chunk.nslots) || (scaled <= dset->shared->cache.chunk.nslots && - dset->shared->cache.chunk.scaled_dims[u] > dset->shared->cache.chunk.nslots)) + dset->shared->cache.chunk.scaled_dims[dim_idx] > dset->shared->cache.chunk.nslots)) update_chunks = TRUE; - if( !(scaled_power2up = H5VM_power2up(scaled)) ) + if(!(scaled_power2up = H5VM_power2up(scaled))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get the next power of 2") /* Check if the number of bits required to encode the scaled size value changed */ - if(dset->shared->cache.chunk.scaled_power2up[u] != scaled_power2up) { + if(dset->shared->cache.chunk.scaled_power2up[dim_idx] != scaled_power2up) { /* Update the 'power2up' & 'encode_bits' values for the current dimension */ - dset->shared->cache.chunk.scaled_power2up[u] = scaled_power2up; - dset->shared->cache.chunk.scaled_encode_bits[u] = H5VM_log2_gen(scaled_power2up); + dset->shared->cache.chunk.scaled_power2up[dim_idx] = scaled_power2up; + dset->shared->cache.chunk.scaled_encode_bits[dim_idx] = H5VM_log2_gen(scaled_power2up); /* Indicate that the cached chunk indices need to be updated */ update_chunks = TRUE; @@ -2830,7 +3102,7 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) } /* end if */ /* Update the cached copy of the dataset's dimensions */ - dset->shared->curr_dims[u] = size[u]; + dset->shared->curr_dims[dim_idx] = size[dim_idx]; } /* end for */ /*------------------------------------------------------------------------- @@ -2846,7 +3118,7 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) /* 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) + if(H5D__chunk_update_cache(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices") } /* end if */ @@ -2860,13 +3132,13 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) 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") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") dset->shared->layout.storage.u.virt.list[u].virtual_space_status = H5O_VIRTUAL_STATUS_CORRECT; /* Patch sub-source datasets */ - for(v = 0; v < dset->shared->layout.storage.u.virt.list[u].sub_dset_nalloc; v++) + for(v = 0; v < dset->shared->layout.storage.u.virt.list[u].sub_dset_nused; 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") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") } /* end for */ /* Mark virtual datasets as not fully initialized so internal @@ -2879,8 +3151,6 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) 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") @@ -2892,44 +3162,41 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) *------------------------------------------------------------------------- */ if(H5D_CHUNKED == dset->shared->layout.type) { - if(shrink && (*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)) + if(shrink && ((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage) + || (dset->shared->layout.ops->is_data_cached && (*dset->shared->layout.ops->is_data_cached)(dset->shared)))) /* Remove excess chunks */ - if(H5D__chunk_prune_by_extent(dset, dxpl_id, curr_dims) < 0) + if(H5D__chunk_prune_by_extent(dset, curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks") /* Update chunks that are no longer edge chunks as a result of * expansion */ if(expand && (dset->shared->layout.u.chunk.flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) && (dset->shared->dcpl_cache.pline.nused > 0)) - if(H5D__chunk_update_old_edge_chunks(dset, dxpl_id, curr_dims) < 0) + if(H5D__chunk_update_old_edge_chunks(dset, curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to do update old edge chunks") - } /* end if */ + } /* end if */ /* Mark the dataspace as dirty, for later writing to the file */ - if(H5D__mark(dset, dxpl_id, H5D_MARK_SPACE) < 0) + if(H5D__mark(dset, H5D_MARK_SPACE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to mark dataspace as dirty") } /* end if */ done: - FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL) + FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__set_extent() */ /*------------------------------------------------------------------------- - * Function: H5D__flush_sieve_buf - * - * Purpose: Flush any dataset sieve buffer info cached in memory + * Function: H5D__flush_sieve_buf * - * Return: Success: Non-negative - * Failure: Negative - * - * Programmer: Quincey Koziol - * July 27, 2009 + * Purpose: Flush any dataset sieve buffer info cached in memory * + * Return: Success: Non-negative + * Failure: Negative *------------------------------------------------------------------------- */ herr_t -H5D__flush_sieve_buf(H5D_t *dataset, hid_t dxpl_id) +H5D__flush_sieve_buf(H5D_t *dataset) { herr_t ret_value = SUCCEED; /* Return value */ @@ -2943,8 +3210,8 @@ H5D__flush_sieve_buf(H5D_t *dataset, hid_t dxpl_id) 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) + if(H5F_shared_block_write(H5F_SHARED(dataset->oloc.file), H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, + dataset->shared->cache.contig.sieve_size, dataset->shared->cache.contig.sieve_buf) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") /* Reset sieve buffer dirty flag */ @@ -2957,68 +3224,91 @@ done: /*------------------------------------------------------------------------- - * Function: H5D__flush_real - * - * Purpose: Flush any dataset information cached in memory - * - * Return: Success: Non-negative - * Failure: Negative + * Function: H5D__flush_real * - * Programmer: Quincey Koziol - * December 6, 2007 + * Purpose: Flush any dataset information cached in memory * + * Return: Success: Non-negative + * Failure: Negative *------------------------------------------------------------------------- */ herr_t -H5D__flush_real(H5D_t *dataset, hid_t dxpl_id) +H5D__flush_real(H5D_t *dataset) { herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_PACKAGE_TAG(dxpl_id, dataset->oloc.addr, FAIL) + FUNC_ENTER_PACKAGE_TAG(dataset->oloc.addr) /* Check args */ HDassert(dataset); HDassert(dataset->shared); /* Avoid flushing the dataset (again) if it's closing */ - if(!dataset->shared->closing) { + 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) + if(dataset->shared->layout.ops->flush && (dataset->shared->layout.ops->flush)(dataset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush raw data") - } /* end if */ done: - FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL) + FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__flush_real() */ /*------------------------------------------------------------------------- - * Function: H5D__format_convert + * Function: H5D__flush * - * Purpose: For chunked: downgrade the chunk indexing type to version 1 B-tree - * For compact/contiguous: downgrade layout version to 3 + * Purpose: Flush dataset information cached in memory * - * Return: Success: Non-negative - * Failure: Negative + * Return: Success: Non-negative + * Failure: Negative + *------------------------------------------------------------------------- + */ +herr_t +H5D__flush(H5D_t *dset, hid_t dset_id) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check args */ + HDassert(dset); + HDassert(dset->shared); + + /* Flush any dataset information still cached in memory */ + if(H5D__flush_real(dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush cached dataset info") + + /* Flush object's metadata to file */ + if(H5O_flush_common(&dset->oloc, dset_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush dataset and object flush callback") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__flush() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__format_convert * - * Programmer: Vailin Choi - * Feb 2015 + * Purpose: For chunked: downgrade the chunk indexing type to version 1 B-tree + * For compact/contiguous: downgrade layout version to 3 * + * Return: Success: Non-negative + * Failure: Negative *------------------------------------------------------------------------- */ herr_t -H5D__format_convert(H5D_t *dataset, hid_t dxpl_id) +H5D__format_convert(H5D_t *dataset) { - H5D_chk_idx_info_t new_idx_info; /* Index info for the new layout */ - H5D_chk_idx_info_t idx_info; /* Index info for the current layout */ + H5D_chk_idx_info_t new_idx_info; /* Index info for the new layout */ + H5D_chk_idx_info_t idx_info; /* Index info for the current layout */ H5O_layout_t *newlayout = NULL; /* The new layout */ hbool_t init_new_index = FALSE; /* Indicate that the new chunk index is initialized */ - hbool_t delete_old_layout = FALSE; /* Indicate that the old layout message is deleted */ + hbool_t 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 */ + herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_PACKAGE_TAG(dxpl_id, dataset->oloc.addr, FAIL) + FUNC_ENTER_PACKAGE_TAG(dataset->oloc.addr) /* Check args */ HDassert(dataset); @@ -3032,13 +3322,12 @@ H5D__format_convert(H5D_t *dataset, hid_t dxpl_id) /* 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)); + H5MM_memcpy(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; @@ -3049,7 +3338,6 @@ H5D__format_convert(H5D_t *dataset, hid_t dxpl_id) /* 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; @@ -3066,7 +3354,7 @@ H5D__format_convert(H5D_t *dataset, hid_t dxpl_id) 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 + /* 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) @@ -3074,13 +3362,13 @@ H5D__format_convert(H5D_t *dataset, hid_t dxpl_id) } /* end if */ /* Delete the old "current" layout message */ - if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, FALSE, dxpl_id) < 0) + if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, FALSE) < 0) HGOTO_ERROR(H5E_SYM, H5E_CANTDELETE, FAIL, "unable to delete layout message") delete_old_layout = TRUE; /* Append the new layout message to the object header */ - if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, newlayout, dxpl_id) < 0) + if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, newlayout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout header message") add_new_layout = TRUE; @@ -3090,7 +3378,7 @@ H5D__format_convert(H5D_t *dataset, hid_t dxpl_id) 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)); + H5MM_memcpy(&dataset->shared->layout, newlayout, sizeof(H5O_layout_t)); break; @@ -3098,7 +3386,7 @@ H5D__format_convert(H5D_t *dataset, hid_t dxpl_id) 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) + if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout)) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") break; @@ -3109,7 +3397,7 @@ H5D__format_convert(H5D_t *dataset, hid_t dxpl_id) case H5D_NLAYOUTS: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset layout type") - default: + default: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "unknown dataset layout type") } /* end switch */ @@ -3117,12 +3405,12 @@ 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) + if(H5O_msg_remove(&dataset->oloc, H5O_LAYOUT_ID, H5O_ALL, FALSE) < 0) HDONE_ERROR(H5E_SYM, H5E_CANTDELETE, FAIL, "unable to delete layout message") /* Add back old layout message */ if(delete_old_layout) - if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &dataset->shared->layout, dxpl_id) < 0) + if(H5O_msg_create(&dataset->oloc, H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &dataset->shared->layout) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to add layout header message") /* Clean up v1 b-tree chunk index */ @@ -3133,7 +3421,7 @@ done: 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)) + if(H5AC_expunge_tag_type_metadata(dataset->oloc.file, dataset->oloc.addr, H5AC_BT_ID, H5AC__NO_FLAGS_SET)) HDONE_ERROR(H5E_DATASET, H5E_CANTEXPUNGE, FAIL, "unable to expunge index metadata") } /* end if */ @@ -3146,25 +3434,21 @@ done: if(newlayout != NULL) newlayout = (H5O_layout_t *)H5MM_xfree(newlayout); - FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL) + FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__format_convert() */ /*------------------------------------------------------------------------- - * Function: H5D__mark - * - * Purpose: Mark some aspect of a dataset as dirty + * Function: H5D__mark * - * Return: Success: Non-negative - * Failure: Negative - * - * Programmer: Quincey Koziol - * July 4, 2008 + * Purpose: Mark some aspect of a dataset as dirty * + * Return: Success: Non-negative + * Failure: Negative *------------------------------------------------------------------------- */ herr_t -H5D__mark(const H5D_t *dataset, hid_t H5_ATTR_UNUSED dxpl_id, unsigned flags) +H5D__mark(const H5D_t *dataset, unsigned flags) { H5O_t *oh = NULL; /* Pointer to dataset's object header */ herr_t ret_value = SUCCEED; /* Return value */ @@ -3180,12 +3464,12 @@ H5D__mark(const H5D_t *dataset, hid_t H5_ATTR_UNUSED dxpl_id, unsigned flags) unsigned update_flags = H5O_UPDATE_TIME; /* Modification time flag */ /* Pin the object header */ - if(NULL == (oh = H5O_pin(&dataset->oloc, dxpl_id))) + if(NULL == (oh = H5O_pin(&dataset->oloc))) HGOTO_ERROR(H5E_DATASET, H5E_CANTPIN, FAIL, "unable to pin dataset object header") /* Update the layout on disk, if it's been changed */ if(flags & H5D_MARK_LAYOUT) { - if(H5D__layout_oh_write(dataset, dxpl_id, oh, update_flags) < 0) + if(H5D__layout_oh_write(dataset, oh, update_flags) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout info") /* Reset the "update the modification time" flag, so we only do it once */ @@ -3194,7 +3478,7 @@ H5D__mark(const H5D_t *dataset, hid_t H5_ATTR_UNUSED dxpl_id, unsigned flags) /* 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) + if(H5S_write(dataset->oloc.file, oh, update_flags, dataset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") /* Reset the "update the modification time" flag, so we only do it once */ @@ -3216,105 +3500,87 @@ done: /*------------------------------------------------------------------------- - * Function: H5D__flush_cb + * Function: H5D__flush_all_cb * - * Purpose: Flush any dataset information cached in memory - * - * Return: Success: Non-negative - * Failure: Negative - * - * Programmer: Quincey Koziol - * November 8, 2007 + * Purpose: Flush any dataset information cached in memory * + * Return: Success: Non-negative + * Failure: Negative *------------------------------------------------------------------------- */ static int -H5D__flush_cb(void *_dataset, hid_t H5_ATTR_UNUSED id, void *_udata) +H5D__flush_all_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 */ + H5D_t *dataset = (H5D_t *)_dataset; /* Dataset pointer */ + H5F_t *f = (H5F_t *)_udata; /* User data for callback */ + int ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_STATIC /* Check args */ HDassert(dataset); + HDassert(f); /* Check for dataset in same file */ - if(udata->f == dataset->oloc.file) { + if(f == dataset->oloc.file) /* Flush the dataset's information */ - if(H5D__flush_real(dataset, udata->dxpl_id) < 0) + if(H5D__flush_real(dataset) < 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() */ +} /* end H5D__flush_all_cb() */ /*------------------------------------------------------------------------- - * Function: H5D_flush + * Function: H5D_flush_all * - * Purpose: Flush any dataset information cached in memory - * - * Return: Success: Non-negative - * Failure: Negative - * - * Programmer: Ray Lu - * August 14, 2002 + * Purpose: Flush any dataset information cached in memory * + * Return: Success: Non-negative + * Failure: Negative *------------------------------------------------------------------------- */ herr_t -H5D_flush(const H5F_t *f, hid_t dxpl_id) +H5D_flush_all(H5F_t *f) { - H5D_flush_ud_t udata; /* User data for callback */ - herr_t ret_value = SUCCEED; /* Return value */ + 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) + if(H5I_iterate(H5I_DATASET, H5D__flush_all_cb, f, FALSE) < 0) /* Casting away const OK -QAK */ HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to flush cached dataset info") done: FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_flush() */ +} /* end H5D_flush_all() */ /*------------------------------------------------------------------------- - * Function: H5D_get_create_plist - * - * Purpose: Private function for H5Dget_create_plist + * Function: H5D_get_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 + * Purpose: Private function for H5Dget_create_plist * + * Return: Success: ID for a copy of the dataset creation + * property list. The template should be + * released by calling H5P_close(). + * Failure: FAIL *------------------------------------------------------------------------- */ hid_t -H5D_get_create_plist(H5D_t *dset) +H5D_get_create_plist(const H5D_t *dset) { H5P_genplist_t *dcpl_plist; /* Dataset's DCPL */ H5P_genplist_t *new_plist; /* Copy of dataset's DCPL */ H5O_layout_t copied_layout; /* Layout to tweak */ H5O_fill_t copied_fill; /* Fill value to tweak */ H5O_efl_t copied_efl; /* External file list to tweak */ - hid_t new_dcpl_id = FAIL; - hid_t ret_value = H5I_INVALID_HID; /* Return value */ + hid_t new_dcpl_id = FAIL; + hid_t ret_value = H5I_INVALID_HID; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -3329,7 +3595,7 @@ H5D_get_create_plist(H5D_t *dset) 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) + if(H5O_get_create_plist(&dset->oloc, new_plist) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get object creation info") /* Get the layout property */ @@ -3355,7 +3621,7 @@ H5D_get_create_plist(H5D_t *dset) /* 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 */ + /* 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") @@ -3391,7 +3657,7 @@ H5D_get_create_plist(H5D_t *dset) 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))) + if(NULL == (tpath = H5T_path_find(dset->shared->type, copied_fill.type))) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types") /* Convert disk form of fill value into memory form */ @@ -3419,7 +3685,7 @@ H5D_get_create_plist(H5D_t *dset) } /* 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) { + if(H5T_convert(tpath, src_id, dst_id, (size_t)1, (size_t)0, (size_t)0, copied_fill.buf, bkg_buf) < 0) { H5I_dec_ref(src_id); H5I_dec_ref(dst_id); if(bkg_buf) @@ -3472,39 +3738,38 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_get_access_plist - * - * Purpose: Returns a copy of the dataset access property list. + * Function: H5D_get_access_plist * - * Return: Success: ID for a copy of the dataset access - * property list. - * - * Failure: FAIL - * - * Programmer: Mohamad Chaarawi - * March, 2012 + * Purpose: Returns a copy of the dataset access property list. * + * Return: Success: ID for a copy of the dataset access + * property list. + * Failure: FAIL *------------------------------------------------------------------------- */ hid_t -H5D_get_access_plist(H5D_t *dset) +H5D_get_access_plist(const H5D_t *dset) { - H5P_genplist_t *old_plist; /* Default DAPL */ + H5P_genplist_t *old_plist; /* Stored DAPL from dset */ H5P_genplist_t *new_plist; /* New DAPL */ + H5P_genplist_t *def_fapl; /* Default FAPL */ + H5D_append_flush_t def_append_flush_info = {0}; /* Default append flush property */ + H5D_rdcc_t def_chunk_info; /* Default chunk cache property */ 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") + /* Make a copy of the dataset's dataset access property list */ + if(NULL == (old_plist = (H5P_genplist_t *)H5I_object(dset->shared->dapl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get 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") + HGOTO_ERROR(H5E_PLIST, 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 the dataset is chunked then copy the rdcc & append flush parameters. + * Otherwise, use the default values. */ 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") @@ -3514,7 +3779,33 @@ H5D_get_access_plist(H5D_t *dset) 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 */ + } else { + /* Get the default FAPL */ + if(NULL == (def_fapl = (H5P_genplist_t *)H5I_object(H5P_LST_FILE_ACCESS_ID_g))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not a property list") + + /* Set the data cache number of slots to the value of the default FAPL */ + if (H5P_get(def_fapl, H5D_ACS_DATA_CACHE_NUM_SLOTS_NAME, &def_chunk_info.nslots) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET,FAIL, "can't get data number of slots"); + if(H5P_set(new_plist, H5D_ACS_DATA_CACHE_NUM_SLOTS_NAME, &def_chunk_info.nslots) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set data cache number of slots") + + /* Set the data cache byte size to the value of the default FAPL */ + if (H5P_get(def_fapl, H5D_ACS_DATA_CACHE_BYTE_SIZE_NAME, &def_chunk_info.nbytes_max) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET,FAIL, "can't get data cache byte size"); + if(H5P_set(new_plist, H5D_ACS_DATA_CACHE_BYTE_SIZE_NAME, &def_chunk_info.nbytes_max) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set data cache byte size") + + /* Set the preempt read chunks property to the value of the default FAPL */ + if (H5P_get(def_fapl, H5D_ACS_PREEMPT_READ_CHUNKS_NAME, &def_chunk_info.w0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET,FAIL, "can't get preempt read chunks"); + if(H5P_set(new_plist, H5D_ACS_PREEMPT_READ_CHUNKS_NAME, &def_chunk_info.w0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set preempt read chunks") + + /* Set the append flush property to its default value */ + if(H5P_set(new_plist, H5D_ACS_APPEND_FLUSH_NAME, &def_append_flush_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set append flush property") + }/* end if-else */ /* 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) @@ -3522,6 +3813,10 @@ H5D_get_access_plist(H5D_t *dset) if(H5P_set(new_plist, H5D_ACS_VDS_PRINTF_GAP_NAME, &(dset->shared->layout.storage.u.virt.printf_gap)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set VDS printf gap") + /* Set the vds prefix option */ + if(H5P_set(new_plist, H5D_ACS_VDS_PREFIX_NAME, &(dset->shared->vds_prefix)) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set vds prefix") + /* Set the external file prefix option */ if(H5P_set(new_plist, H5D_ACS_EFILE_PREFIX_NAME, &(dset->shared->extfile_prefix)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set external file prefix") @@ -3530,46 +3825,40 @@ H5D_get_access_plist(H5D_t *dset) ret_value = new_dapl_id; done: - if(ret_value < 0) { + 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. + * Function: H5D__get_space * - * Return: Success: ID for dataspace - * - * Failure: FAIL - * - * Programmer: Mohamad Chaarawi - * March, 2012 + * Purpose: Returns and ID for the dataspace of the dataset. * + * Return: Success: ID for dataspace + * Failure: FAIL *------------------------------------------------------------------------- */ hid_t -H5D_get_space(H5D_t *dset) +H5D__get_space(const H5D_t *dset) { - H5S_t *space = NULL; - hid_t ret_value = H5I_INVALID_HID; + H5S_t *space = NULL; + hid_t ret_value = H5I_INVALID_HID; - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_PACKAGE /* If the layout is virtual, update the extent */ if(dset->shared->layout.type == H5D_VIRTUAL) - if(H5D__virtual_set_extent_unlim(dset, H5AC_ind_read_dxpl_id) < 0) + if(H5D__virtual_set_extent_unlim(dset) < 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 */ + /* Read the dataspace message and return a dataspace object */ if(NULL == (space = H5S_copy(dset->shared->space, FALSE, TRUE))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get data space") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get dataspace") /* Create an atom */ if((ret_value = H5I_register(H5I_DATASPACE, space, TRUE)) < 0) @@ -3582,37 +3871,33 @@ done: HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_get_space() */ +} /* end H5D__get_space() */ /*------------------------------------------------------------------------- - * Function: H5D_get_type - * - * Purpose: Returns and ID for the datatype of the dataset. - * - * Return: Success: ID for datatype + * Function: H5D__get_type * - * Failure: FAIL + * Purpose: Returns and ID for the datatype of the dataset. * - * Programmer: Mohamad Chaarawi - * March, 2012 + * Return: Success: ID for datatype + * Failure: FAIL * *------------------------------------------------------------------------- */ hid_t -H5D_get_type(H5D_t *dset) +H5D__get_type(const H5D_t *dset) { - H5T_t *dt = NULL; - hid_t ret_value = FAIL; + H5T_t *dt = NULL; + hid_t ret_value = FAIL; - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_PACKAGE /* Patch the datatype's "top level" file pointer */ if(H5T_patch_file(dset->shared->type, dset->oloc.file) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to patch datatype's file pointer") /* Copy the dataset's datatype */ - if(NULL == (dt = H5T_copy(dset->shared->type, H5T_COPY_REOPEN))) + if(NULL == (dt = H5T_copy_reopen(dset->shared->type))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy datatype") /* Mark any datatypes as being in memory now */ @@ -3623,39 +3908,44 @@ H5D_get_type(H5D_t *dset) 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") + /* Create an atom */ + if(H5T_is_named(dt)) { + /* If this is a committed datatype, we need to recreate the + * two-level IDs, where the VOL object is a copy of the + * returned datatype. + */ + if((ret_value = H5VL_wrap_register(H5I_DATATYPE, dt, TRUE)) < 0) + HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register datatype") + } /* end if */ + else + 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(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() */ +} /* end H5D__get_type() */ /*------------------------------------------------------------------------- - * Function: H5D__refresh + * Function: H5D__refresh * - * Purpose: Refreshes all buffers associated with a dataset. - * - * Return: SUCCEED/FAIL - * - * Programmer: Dana Robinson - * November 2015 + * Purpose: Refreshes all buffers associated with a dataset. * + * Return: SUCCEED/FAIL *------------------------------------------------------------------------- */ herr_t -H5D__refresh(hid_t dset_id, H5D_t *dset, hid_t dxpl_id) +H5D__refresh(hid_t dset_id, H5D_t *dset) { H5D_virtual_held_file_t *head = NULL; /* Pointer to list of files held open */ hbool_t virt_dsets_held = FALSE; /* Whether virtual datasets' files are held open */ herr_t ret_value = SUCCEED; /* Return value */ - FUNC_ENTER_NOAPI_NOINIT + FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(dset); @@ -3669,21 +3959,19 @@ H5D__refresh(hid_t dset_id, H5D_t *dset, hid_t dxpl_id) virt_dsets_held = TRUE; /* Refresh source datasets for virtual dataset */ - if(H5D__virtual_refresh_source_dsets(dset, dxpl_id) < 0) + if(H5D__virtual_refresh_source_dsets(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to refresh VDS source datasets") } /* end if */ - + /* Refresh dataset object */ - if((H5O_refresh_metadata(dset_id, dset->oloc, dxpl_id)) < 0) + if((H5O_refresh_metadata(dset_id, dset->oloc)) < 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 */ + /* Release hold on (source) virtual datasets' files */ + if(virt_dsets_held) if(H5D__virtual_release_source_dset_files(head) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't release VDS source files held open") - } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__refresh() */ |