diff options
| -rw-r--r-- | MANIFEST | 2 | ||||
| -rw-r--r-- | src/H5D.c | 2377 | ||||
| -rw-r--r-- | src/H5Ddbg.c | 123 | ||||
| -rw-r--r-- | src/H5Ddeprec.c | 28 | ||||
| -rw-r--r-- | src/H5Dfill.c | 2 | ||||
| -rw-r--r-- | src/H5Dint.c | 2425 | ||||
| -rw-r--r-- | src/H5Dio.c | 4 | ||||
| -rw-r--r-- | src/H5Dpkg.h | 31 | ||||
| -rwxr-xr-x | src/Makefile.am | 4 | ||||
| -rw-r--r-- | src/Makefile.in | 6 |
10 files changed, 2607 insertions, 2395 deletions
@@ -452,9 +452,11 @@ ./src/H5D.c ./src/H5Dcompact.c ./src/H5Dcontig.c +./src/H5Ddbg.c ./src/H5Ddeprec.c ./src/H5Defl.c ./src/H5Dfill.c +./src/H5Dint.c ./src/H5Dio.c ./src/H5Distore.c ./src/H5Dmpio.c @@ -20,7 +20,7 @@ #define H5D_PACKAGE /*suppress error about including H5Dpkg */ /* Interface initialization */ -#define H5_INTERFACE_INIT_FUNC H5D_init_interface +#define H5_INTERFACE_INIT_FUNC H5D_init_pub_interface /***********/ @@ -29,12 +29,8 @@ #include "H5private.h" /* Generic Functions */ #include "H5Dpkg.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ -#include "H5FOprivate.h" /* File objects */ -#include "H5HLprivate.h" /* Local heaps */ +#include "H5FLprivate.h" /* Free lists */ #include "H5Iprivate.h" /* IDs */ -#include "H5Lprivate.h" /* Links */ -#include "H5MMprivate.h" /* Memory management */ -#include "H5Vprivate.h" /* Vectors and arrays */ /****************/ @@ -46,44 +42,21 @@ /* Local Typedefs */ /******************/ -/* Internal data structure for computing variable-length dataset's total size */ -typedef struct { - hid_t dataset_id; /* ID of the dataset we are working on */ - hid_t fspace_id; /* ID of the file dataset's dataspace we are working on */ - hid_t mspace_id; /* ID of the memory dataset's dataspace we are working on */ - 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 */ - hid_t xfer_pid; /* ID of the dataset xfer property list */ - hsize_t size; /* Accumulated number of bytes for the selection */ -} H5D_vlen_bufsize_t; - /********************/ /* Local Prototypes */ /********************/ -/* General stuff */ -static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite, hid_t dxpl_id); -static H5D_shared_t *H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type); -static herr_t H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, - const H5T_t *type); -static herr_t H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space); -static herr_t H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset); -static herr_t H5D_open_oid(H5D_t *dataset, hid_t dxpl_id); -static herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id); -static hsize_t H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id); -static haddr_t H5D_get_offset(const H5D_t *dset); -static herr_t H5D_iterate(void *buf, hid_t type_id, H5S_t *space, - H5D_operator_t op, void *operator_data); -static herr_t H5D_set_extent(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id); - /*********************/ /* Package Variables */ /*********************/ -/* Define a "default" dataset transfer property list cache structure to use for default DXPLs */ -H5D_dxpl_cache_t H5D_def_dxpl_cache; +/* Declare extern the free list to manage blocks of VL data */ +H5FL_BLK_EXTERN(vlen_vl_buf); + +/* Declare extern the free list to manage other blocks of VL data */ +H5FL_BLK_EXTERN(vlen_fl_buf); /*****************************/ @@ -98,166 +71,27 @@ H5FL_BLK_EXTERN(type_conv); /* Local Variables */ /*******************/ -/* Declare a free list to manage the H5D_t and H5D_shared_t structs */ -H5FL_DEFINE_STATIC(H5D_t); -H5FL_DEFINE_STATIC(H5D_shared_t); - -/* Declare a free list to manage blocks of VL data */ -H5FL_BLK_DEFINE_STATIC(vlen_vl_buf); - -/* Declare a free list to manage other blocks of VL data */ -H5FL_BLK_DEFINE_STATIC(vlen_fl_buf); - -/* Declare the external PQ free list for the sieve buffer information */ -H5FL_BLK_EXTERN(sieve_buf); - -/* Define a static "default" dataset structure to use to initialize new datasets */ -static H5D_shared_t H5D_def_dset; - - - -/*------------------------------------------------------------------------- - * Function: H5D_init - * - * Purpose: Initialize the interface from some other layer. - * - * Return: Success: non-negative - * - * Failure: negative - * - * Programmer: Quincey Koziol - * Saturday, March 4, 2000 - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_init(void) -{ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_init, FAIL) - /* FUNC_ENTER() does all the work */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_init() */ /*-------------------------------------------------------------------------- NAME - H5D_init_interface -- Initialize interface-specific information + H5D_init_pub_interface -- Initialize interface-specific information USAGE - herr_t H5D_init_interface() - + herr_t H5D_init_pub_interface() RETURNS Non-negative on success/Negative on failure DESCRIPTION - Initializes any interface-specific data or routines. -NOTES - Care must be taken when using the H5P functions, since they can cause - a deadlock in the library when the library is attempting to terminate -QAK + Initializes any interface-specific data or routines. (Just calls + H5D_init() currently). --------------------------------------------------------------------------*/ static herr_t -H5D_init_interface(void) +H5D_init_pub_interface(void) { - H5P_genplist_t *def_dcpl; /* Default Dataset Creation Property list */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_init_interface) - - /* Initialize the atom group for the dataset IDs */ - if(H5I_register_type(H5I_DATASET, (size_t)H5I_DATASETID_HASHSIZE, H5D_RESERVED_ATOMS, (H5I_free_t)H5D_close)<H5I_FILE) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize interface") - - /* Reset the "default dataset" information */ - HDmemset(&H5D_def_dset, 0, sizeof(H5D_shared_t)); - - /* Get the default dataset creation property list values and initialize the - * default dataset with them. - */ - if(NULL == (def_dcpl = (H5P_genplist_t *)H5I_object(H5P_LST_DATASET_CREATE_g))) - HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get default dataset creation property list") + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_init_pub_interface) - /* Get the default data storage method */ - if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout.type) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve layout") - - /* Get the default dataset creation properties */ - if(H5P_get(def_dcpl, H5D_CRT_EXT_FILE_LIST_NAME, &H5D_def_dset.dcpl_cache.efl) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve external file list") - if(H5P_get(def_dcpl, H5D_CRT_FILL_VALUE_NAME, &H5D_def_dset.dcpl_cache.fill) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value") - if(H5P_get(def_dcpl, H5D_CRT_DATA_PIPELINE_NAME, &H5D_def_dset.dcpl_cache.pline) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve pipeline filter") - - /* Reset the "default DXPL cache" information */ - HDmemset(&H5D_def_dxpl_cache, 0, sizeof(H5D_dxpl_cache_t)); - - /* Get the default DXPL cache information */ - if(H5D_get_dxpl_cache_real(H5P_DATASET_XFER_DEFAULT, &H5D_def_dxpl_cache) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve default DXPL info") - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_init_interface() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_term_interface - * - * Purpose: Terminate this interface. - * - * Return: Success: Positive if anything was done that might - * affect other interfaces; zero otherwise. - * - * Failure: Negative. - * - * Programmer: Robb Matzke - * Friday, November 20, 1998 - * - *------------------------------------------------------------------------- - */ -int -H5D_term_interface(void) -{ - int n=0; - - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_term_interface) - - if(H5_interface_initialize_g) { - if((n=H5I_nmembers(H5I_DATASET))>0) { - /* The dataset API uses the "force" flag set to true because it - * is using the "file objects" (H5FO) API functions to track open - * objects in the file. Using the H5FO code means that dataset - * IDs can have reference counts >1, when an existing dataset is - * opened more than once. However, the H5I code does not attempt - * to close objects with reference counts>1 unless the "force" flag - * is set to true. - * - * At some point (probably after the group and datatypes use the - * the H5FO code), the H5FO code might need to be switched around - * to storing pointers to the objects being tracked (H5D_t, H5G_t, - * etc) and reference count those itself instead of relying on the - * reference counting in the H5I layer. Then, the "force" flag can - * be put back to false. - * - * Setting the "force" flag to true for all the interfaces won't - * work because the "file driver" (H5FD) APIs use the H5I reference - * counting to avoid closing a file driver out from underneath an - * open file... - * - * QAK - 5/13/03 - */ - H5I_clear_type(H5I_DATASET, TRUE); - } else { - H5I_dec_type_ref(H5I_DATASET); - H5_interface_initialize_g = 0; - n = 1; /*H5I*/ - } - } - FUNC_LEAVE_NOAPI(n) -} /* end H5D_term_interface() */ + FUNC_LEAVE_NOAPI(H5D_init()) +} /* H5D_init_pub_interface() */ /*------------------------------------------------------------------------- @@ -348,64 +182,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_create_named - * - * Purpose: Internal routine to create a new dataset. - * - * Return: Success: Non-NULL, pointer to new dataset object. - * - * Failure: NULL - * - * Programmer: Quincey Koziol - * Thursday, April 5, 2007 - * - *------------------------------------------------------------------------- - */ -H5D_t * -H5D_create_named(const H5G_loc_t *loc, const char *name, hid_t type_id, - const H5S_t *space, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id, - hid_t dxpl_id) -{ - H5O_obj_create_t ocrt_info; /* Information for object creation */ - H5D_obj_create_t dcrt_info; /* Information for dataset creation */ - H5D_t *ret_value; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_create_named, NULL) - - /* Check arguments */ - HDassert(loc); - HDassert(name && *name); - HDassert(type_id != H5P_DEFAULT); - HDassert(space); - HDassert(lcpl_id != H5P_DEFAULT); - HDassert(dcpl_id != H5P_DEFAULT); - HDassert(dapl_id != H5P_DEFAULT); - HDassert(dxpl_id != H5P_DEFAULT); - - /* Set up dataset creation info */ - dcrt_info.type_id = type_id; - dcrt_info.space = space; - dcrt_info.dcpl_id = dcpl_id; - - /* Set up object creation information */ - ocrt_info.obj_type = H5O_TYPE_DATASET; - ocrt_info.crt_info = &dcrt_info; - ocrt_info.new_obj = NULL; - - /* Create the new dataset and link it to its parent group */ - if(H5L_link_object(loc, name, &ocrt_info, lcpl_id, dapl_id, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to create and link to dataset") - HDassert(ocrt_info.new_obj); - - /* Set the return value */ - ret_value = (H5D_t *)ocrt_info.new_obj; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_create_named() */ - - -/*------------------------------------------------------------------------- * Function: H5Dcreate_anon * * Purpose: Creates a new dataset named NAME at LOC_ID, opens the @@ -701,70 +477,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_get_space_status - * - * Purpose: Returns the status of data space allocation. - * - * Return: - * Success: Non-negative - * - * Failture: Negative - * - * Programmer: Raymond Lu - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id) -{ - H5S_t *space; /* Dataset's dataspace */ - hsize_t space_allocated; /* The number of bytes allocated for chunks */ - hssize_t total_elem; /* The total number of elements in dataspace */ - size_t type_size; /* The size of the datatype for the dataset */ - hsize_t full_size; /* The number of bytes in the dataset when fully populated */ - herr_t ret_value = SUCCEED; - - FUNC_ENTER_NOAPI_NOINIT(H5D_get_space_status) - - HDassert(dset); - - /* Get the dataset's dataspace */ - space = dset->shared->space; - HDassert(space); - - /* Get the total number of elements in dataset's dataspace */ - if((total_elem=H5S_GET_EXTENT_NPOINTS(space)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get # of dataspace elements") - - /* Get the size of the dataset's datatype */ - if((type_size = H5T_get_size(dset->shared->type)) == 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get size of datatype") - - /* Compute the maximum size of the dataset in bytes */ - H5_CHECK_OVERFLOW(total_elem,hssize_t,hsize_t); - full_size=((hsize_t)total_elem)*type_size; - - /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */ - space_allocated = H5D_get_storage_size(dset, dxpl_id); - - /* Decide on how much of the space is allocated */ - if(space_allocated == 0) - *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED; - else if(space_allocated == full_size) - *allocation = H5D_SPACE_STATUS_ALLOCATED; - else { - /* Should only happen for chunked datasets currently */ - HDassert(dset->shared->layout.type == H5D_CHUNKED); - - *allocation = H5D_SPACE_STATUS_PART_ALLOCATED; - } /* end else */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_get_space_status() */ - - -/*------------------------------------------------------------------------- * Function: H5Dget_type * * Purpose: Returns a copy of the file datatype for a dataset. @@ -942,1539 +654,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_new - * - * Purpose: Creates a new, empty dataset structure - * - * Return: Success: Pointer to a new dataset descriptor. - * - * Failure: NULL - * - * Programmer: Quincey Koziol - * Monday, October 12, 1998 - * - *------------------------------------------------------------------------- - */ -static H5D_shared_t * -H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) -{ - H5P_genplist_t *plist; /* Property list created */ - H5D_shared_t *new_dset = NULL; /* New dataset object */ - H5D_shared_t *ret_value; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_new) - - /* Allocate new shared dataset structure */ - if(NULL == (new_dset = H5FL_MALLOC(H5D_shared_t))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - - /* Copy the default dataset information */ - HDmemcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t)); - - /* If we are using the default dataset creation property list, during creation - * don't bother to copy it, just increment the reference count - */ - if(!vl_type && creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) { - if(H5I_inc_ref(dcpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "Can't increment default DCPL ID") - new_dset->dcpl_id = dcpl_id; - } /* end if */ - else { - /* Get the property list */ - if(NULL == (plist = (H5P_genplist_t *)H5I_object(dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list") - - new_dset->dcpl_id = H5P_copy_plist(plist); - } /* end else */ - - /* Set return value */ - ret_value = new_dset; - -done: - if(ret_value == NULL) - if(new_dset != NULL) { - if(new_dset->dcpl_id != 0) - (void)H5I_dec_ref(new_dset->dcpl_id); - H5FL_FREE(H5D_shared_t, new_dset); - } /* end if */ - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_new() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_init_type - * - * Purpose: Copy a datatype for a dataset's use, performing all the - * necessary adjustments, etc. - * - * Return: Success: SUCCEED - * Failure: FAIL - * - * Programmer: Quincey Koziol - * Thursday, June 24, 2004 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, const H5T_t *type) -{ - htri_t relocatable; /* Flag whether the type is relocatable */ - htri_t immutable; /* Flag whether the type is immutable */ - hbool_t use_latest_format; /* Flag indicating the newest file format should be used */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_init_type) - - /* Sanity checking */ - HDassert(file); - HDassert(dset); - HDassert(type); - - /* Check whether the datatype is relocatable */ - if((relocatable = H5T_is_relocatable(type)) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?") - - /* Check whether the datatype is immutable */ - if((immutable = H5T_is_immutable(type)) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?") - - /* Get the file's 'use the latest version of the format' flag */ - use_latest_format = H5F_USE_LATEST_FORMAT(file); - - /* Copy the datatype if it's a custom datatype or if it'll change when it's location is changed */ - if(!immutable || relocatable || use_latest_format) { - /* Copy datatype for dataset */ - if((dset->shared->type = H5T_copy(type, H5T_COPY_ALL)) == NULL) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy datatype") - - /* Mark any datatypes as being on disk now */ - if(H5T_set_loc(dset->shared->type, file, H5T_LOC_DISK) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't set datatype location") - - /* Set the latest format, if requested */ - if(use_latest_format) - if(H5T_set_latest_version(dset->shared->type) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype") - - /* Get a datatype ID for the dataset's datatype */ - if((dset->shared->type_id = H5I_register(H5I_DATATYPE, dset->shared->type)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") - } /* end if */ - /* Not a custom datatype, just use it directly */ - else { - if(H5I_inc_ref(type_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment datatype ID") - - /* Use existing datatype */ - dset->shared->type_id = type_id; - dset->shared->type = (H5T_t *)type; /* (Cast away const OK - QAK) */ - } /* end else */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_init_type() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_init_space - * - * Purpose: Copy a dataspace for a dataset's use, performing all the - * necessary adjustments, etc. - * - * Return: Success: SUCCEED - * Failure: FAIL - * - * Programmer: Quincey Koziol - * Tuesday, July 24, 2007 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space) -{ - hbool_t use_latest_format; /* Flag indicating the newest file format should be used */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_init_space) - - /* Sanity checking */ - HDassert(file); - HDassert(dset); - HDassert(space); - - /* Get the file's 'use the latest version of the format' flag */ - use_latest_format = H5F_USE_LATEST_FORMAT(file); - - /* Copy dataspace for dataset */ - if(NULL == (dset->shared->space = H5S_copy(space, FALSE))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dataspace") - - /* Set the latest format, if requested */ - if(use_latest_format) - if(H5S_set_latest_version(dset->shared->space) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype") - - /* Set the dataset's dataspace to 'all' selection */ - if(H5S_select_all(dset->shared->space, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set all selection") - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_init_space() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_update_oh_info - * - * Purpose: Create and fill object header for dataset - * - * Return: Success: SUCCEED - * Failure: FAIL - * - * Programmer: Bill Wendling - * Thursday, October 31, 2002 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) -{ - struct H5O_t *oh = NULL; /* Pointer to dataset's object header */ - size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ - H5O_loc_t *oloc = NULL; /* Dataset's object location */ - H5O_layout_t *layout; /* Dataset's layout information */ - H5T_t *type; /* Dataset's datatype */ - hbool_t use_latest_format; /* Flag indicating the newest file format should be used */ - H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ - H5D_fill_value_t fill_status; /* Fill value status */ - hbool_t fill_changed = FALSE; /* Flag indicating the fill value was changed */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_update_oh_info) - - /* Sanity checking */ - HDassert(file); - HDassert(dset); - - /* Set some local variables, for convenience */ - oloc = &dset->oloc; - layout = &dset->shared->layout; - type = dset->shared->type; - fill_prop = &dset->shared->dcpl_cache.fill; - - /* Get the file's 'use the latest version of the format' flag */ - use_latest_format = H5F_USE_LATEST_FORMAT(file); - - /* Retrieve "defined" status of fill value */ - if(H5P_is_fill_value_defined(fill_prop, &fill_status) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") - - /* Special case handling for variable-length types */ - if(H5T_detect_class(type, H5T_VLEN)) { - /* If the default fill value is chosen for variable-length types, always write it */ - if(fill_prop->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_DEFAULT) { - /* Update dataset creation property */ - fill_prop->fill_time = H5D_FILL_TIME_ALLOC; - - /* Note that the fill value changed */ - fill_changed = TRUE; - } /* end if */ - - /* Don't allow never writing fill values with variable-length types */ - if(fill_prop->fill_time == H5D_FILL_TIME_NEVER) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Dataset doesn't support VL datatype when fill value is not defined") - } /* end if */ - - /* Determine whether fill value is defined or not */ - if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) { - /* Convert fill value buffer to dataset's datatype */ - if(fill_prop->buf && fill_prop->size > 0 && H5O_fill_convert(fill_prop, type, &fill_changed, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert fill value to dataset type") - - fill_prop->fill_defined = TRUE; - } else if(fill_status == H5D_FILL_VALUE_UNDEFINED) { - fill_prop->fill_defined = FALSE; - } else - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine if fill value is defined") - - /* Check for invalid fill & allocation time setting */ - if(fill_prop->fill_defined == FALSE && fill_prop->fill_time == H5D_FILL_TIME_ALLOC) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "fill value writing on allocation set, but no fill value defined") - - /* Check if the fill value info changed */ - if(fill_changed) { - H5P_genplist_t *dc_plist; /* Dataset's creation property list */ - - /* Get dataset's property list object */ - HDassert(dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT); - if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") - - /* Update dataset creation property */ - if(H5P_set(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value info") - } /* end if */ - - /* Add the dataset's raw data size to the size of the header, if the raw data will be stored as compact */ - if(layout->type == H5D_COMPACT) - ohdr_size += layout->u.compact.size; - - /* Create an object header for the dataset */ - if(H5O_create(file, dxpl_id, ohdr_size, dset->shared->dcpl_id, oloc/*out*/) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header") - - /* Get a pointer to the object header itself */ - if((oh = H5O_protect(oloc, dxpl_id)) == NULL) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to protect dataset object header") - - /* Write new fill value message */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update new fill value header message") - - /* If there is valid information for the old fill value struct, add it */ - /* (only if we aren't trying to write the latest version of the file format) */ - if(fill_prop->buf && !use_latest_format) { - H5O_fill_t old_fill_prop; /* Copy of fill value property, for writing as "old" fill value */ - - /* Shallow copy the fill value property */ - /* (we only want to make certain that the shared component isnt' modified) */ - HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop)); - - /* Reset shared component info */ - H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop); - - /* Write old fill value */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_ID, H5O_MSG_FLAG_CONSTANT, 0, &old_fill_prop) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update old fill value header message") - } /* end if */ - - /* Update the datatype and dataspace header messages */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update datatype header message") - if(H5S_append(file, dxpl_id, oh, dset->shared->space) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message") - - /* Update the filters message, if this is a chunked dataset */ - if(layout->type == H5D_CHUNKED) { - H5O_pline_t *pline; /* Dataset's I/O pipeline information */ - - pline = &dset->shared->dcpl_cache.pline; - if(pline->nused > 0 && H5O_msg_append(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message") - } /* end if */ - - /* - * Allocate storage if space allocate time is early; otherwise delay - * allocation until later. - */ - if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) - if(H5D_alloc_storage(file, dxpl_id, dset, H5D_ALLOC_CREATE, FALSE, FALSE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") - - /* Update external storage message, if it's used */ - if(dset->shared->dcpl_cache.efl.nused > 0) { - H5O_efl_t *efl = &dset->shared->dcpl_cache.efl; /* Dataset's external file list */ - H5HL_t *heap; /* Pointer to local heap for EFL file names */ - size_t heap_size = H5HL_ALIGN(1); - size_t u; - - /* Determine size of heap needed to stored the file names */ - for(u = 0; u < efl->nused; ++u) - heap_size += H5HL_ALIGN(HDstrlen(efl->slot[u].name) + 1); - - /* Create the heap for the EFL file names */ - if(H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr/*out*/) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create EFL file name heap") - - /* Pin the heap down in memory */ - if(NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC_WRITE))) - HGOTO_ERROR(H5E_DATASET, H5E_PROTECT, FAIL, "unable to protect EFL file name heap") - - /* Insert "empty" name first */ - if((size_t)(-1) == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) { - H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr); - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap") - } /* end if */ - - for(u = 0; u < efl->nused; ++u) { - size_t offset; /* Offset of file name in heap */ - - /* Insert file name into heap */ - if((size_t)(-1) == (offset = H5HL_insert(file, dxpl_id, heap, - HDstrlen(efl->slot[u].name) + 1, efl->slot[u].name))) { - H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr); - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap") - } /* end if */ - - /* Store EFL file name offset */ - HDassert(0 == efl->slot[u].name_offset); - efl->slot[u].name_offset = offset; - } /* end for */ - - /* Release the heap */ - if(H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_PROTECT, FAIL, "unable to unprotect EFL file name heap") - heap = NULL; - - /* Insert EFL message into dataset object header */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message") - } /* end if */ - - /* Create layout message */ - /* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */ - /* (Note: this is relying on H5D_alloc_storage not calling H5O_msg_write during dataset creation) */ - if(H5O_msg_append(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout") - -#ifdef H5O_ENABLE_BOGUS -{ - H5P_genplist_t *dc_plist; /* Dataset's creation property list */ - - /* Get dataset's property list object */ - if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") - - /* Check whether to add a "bogus" message */ - if(H5P_exist_plist(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME) > 0) { - uint8_t bogus_flags = 0; /* Flags for creating "bogus" message */ - - /* Retrieve "bogus" message flags */ - if(H5P_get(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME, &bogus_flags) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get bogus message options") - - /* Add a "bogus" message (for error testing). */ - if(H5O_bogus_oh(file, dxpl_id, oh, (unsigned)bogus_flags) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create 'bogus' message") - } /* end if */ -} -#endif /* H5O_ENABLE_BOGUS */ - - /* Add a modification time message. */ - if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message") - -done: - /* Release pointer to object header itself */ - if(oloc != NULL && oh != NULL) - if(H5O_unprotect(oloc, oh) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to unprotect dataset object header") - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_update_oh_info() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_create - * - * Purpose: Creates a new dataset with name NAME in file F and associates - * with it a datatype TYPE for each element as stored in the - * file, dimensionality information or dataspace SPACE, and - * other miscellaneous properties CREATE_PARMS. All arguments - * are deep-copied before being associated with the new dataset, - * so the caller is free to subsequently modify them without - * affecting the dataset. - * - * Return: Success: Pointer to a new dataset - * - * Failure: NULL - * - * Programmer: Robb Matzke - * Thursday, December 4, 1997 - * - *------------------------------------------------------------------------- - */ -H5D_t * -H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, - hid_t dxpl_id) -{ - const H5T_t *type; /* Datatype for dataset */ - H5D_t *new_dset = NULL; - int i, ndims; - unsigned chunk_ndims = 0; /* Dimensionality of chunk */ - H5P_genplist_t *dc_plist = NULL; /* New Property list */ - hbool_t has_vl_type = FALSE; /* Flag to indicate a VL-type for dataset */ - hbool_t chunk_init = FALSE; /* Flag to indicate that chunk information was initialized */ - H5G_loc_t dset_loc; /* Dataset location */ - unsigned u; /* Local index variable */ - H5D_t *ret_value; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_create, NULL) - - /* check args */ - HDassert(file); - HDassert(H5I_DATATYPE==H5I_get_type(type_id)); - HDassert(space); - HDassert(H5I_GENPROP_LST==H5I_get_type(dcpl_id)); - HDassert(H5I_GENPROP_LST==H5I_get_type(dxpl_id)); - - /* Get the dataset's datatype */ - if(NULL == (type = (const H5T_t *)H5I_object(type_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a datatype") - - /* Check if the datatype is "sensible" for use in a dataset */ - if(H5T_is_sensible(type) != TRUE) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "datatype is not sensible") - - /* Check if the datatype is/contains a VL-type */ - if(H5T_detect_class(type, H5T_VLEN)) - has_vl_type=TRUE; - - /* Check if the dataspace has an extent set (or is NULL) */ - if(!(H5S_has_extent(space)) ) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "dataspace extent has not been set.") - - /* Initialize the dataset object */ - if(NULL == (new_dset = H5FL_CALLOC(H5D_t))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - - /* Set up & reset dataset location */ - dset_loc.oloc = &(new_dset->oloc); - dset_loc.path = &(new_dset->path); - H5G_loc_reset(&dset_loc); - - /* Initialize the shared dataset space */ - if(NULL == (new_dset->shared = H5D_new(dcpl_id, TRUE, has_vl_type))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - - /* Copy & initialize datatype for dataset */ - if(H5D_init_type(file, new_dset, type_id, type) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy datatype") - - /* Copy & initialize dataspace for dataset */ - if(H5D_init_space(file, new_dset, space) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy dataspace") - - /* Set the dataset's checked_filters flag to enable writing */ - new_dset->shared->checked_filters = TRUE; - - /* Check if the dataset has a non-default DCPL & get important values, if so */ - if(new_dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT) { - H5D_layout_t *layout; /* Dataset's layout information */ - H5O_pline_t *pline; /* Dataset's I/O pipeline information */ - H5O_fill_t *fill; /* Dataset's fill value info */ - - /* Check if the filters in the DCPL can be applied to this dataset */ - if(H5Z_can_apply(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0) - HGOTO_ERROR(H5E_ARGS, H5E_CANTINIT, NULL, "I/O filters can't operate on this dataset") - - /* Make the "set local" filter callbacks for this dataset */ - if(H5Z_set_local(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set local filter parameters") - - /* Get new dataset's property list object */ - if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(new_dset->shared->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list") - - /* Retrieve the properties we need */ - pline = &new_dset->shared->dcpl_cache.pline; - if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, pline) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter") - layout = &new_dset->shared->layout.type; - if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, layout) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout") - if(pline->nused > 0 && H5D_CHUNKED != *layout) - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout") - fill = &new_dset->shared->dcpl_cache.fill; - if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill value info") - - /* Check if the alloc_time is the default and error out */ - if(fill->alloc_time == H5D_ALLOC_TIME_DEFAULT) - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "invalid space allocation state") - - /* Don't allow compact datasets to allocate space later */ - if(*layout == H5D_COMPACT && fill->alloc_time != H5D_ALLOC_TIME_EARLY) - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset must have early space allocation") - - /* If MPI VFD is used, no filter support yet. */ - if(IS_H5FD_MPI(file) && pline->nused > 0) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet") - - /* Chunked datasets are non-default, so retrieve their info here */ - if(H5P_get(dc_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk dimensions") - - /* Get the dataset's external file list information */ - if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &new_dset->shared->dcpl_cache.efl) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list") - } /* end if */ - - /* Set the latest version of the pline & fill messages, if requested */ - if(H5F_USE_LATEST_FORMAT(file)) { - /* Set the latest version for the I/O pipeline message */ - if(H5Z_set_latest_version(&new_dset->shared->dcpl_cache.pline) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of I/O filter pipeline") - - /* Set the latest version for the fill value message */ - if(H5O_fill_set_latest_version(&new_dset->shared->dcpl_cache.fill) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of fill value") - } /* end if */ - - /* Check if this dataset is going into a parallel file and set space allocation time */ - if(IS_H5FD_MPI(file)) - new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY; - - switch(new_dset->shared->layout.type) { - case H5D_CONTIGUOUS: - { - hssize_t tmp_size; /* Temporary holder for raw data size */ - hsize_t dim[H5O_LAYOUT_NDIMS]; /* Current size of data in elements */ - hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */ - - /* - * The maximum size of the dataset cannot exceed the storage size. - * Also, only the slowest varying dimension of a simple data space - * can be extendible (currently only for external data storage). - */ - new_dset->shared->layout.u.contig.addr = HADDR_UNDEF; /* Initialize to no address */ - - if((ndims = H5S_get_simple_extent_dims(new_dset->shared->space, dim, max_dim)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize contiguous storage") - for(i = 1; i < ndims; i++) - if(max_dim[i] > dim[i]) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible") - if(new_dset->shared->dcpl_cache.efl.nused > 0) { - hsize_t max_points = H5S_get_npoints_max(new_dset->shared->space); - hsize_t max_storage = H5O_efl_total_size(&new_dset->shared->dcpl_cache.efl); - - if(H5S_UNLIMITED == max_points) { - if(H5O_EFL_UNLIMITED != max_storage) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unlimited data space but finite storage") - } else if(max_points * H5T_get_size(type) < max_points) { - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space * type size overflowed") - } else if(max_points * H5T_get_size(type) > max_storage) { - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space size exceeds external storage size") - } - - /* Set the I/O functions for this layout type */ - new_dset->shared->io_ops.readvv = H5D_efl_readvv; - new_dset->shared->io_ops.writevv = H5D_efl_writevv; - } /* end if */ - else { - if(ndims > 0 && max_dim[0] > dim[0]) - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset") - - /* Set the I/O functions for this layout type */ - new_dset->shared->io_ops.readvv = H5D_contig_readvv; - new_dset->shared->io_ops.writevv = H5D_contig_writevv; - } /* end else */ - - /* Compute the total size of a chunk */ - tmp_size = H5S_GET_EXTENT_NPOINTS(new_dset->shared->space) * H5T_get_size(new_dset->shared->type); - H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t); - - /* Get the sieve buffer size for this dataset */ - new_dset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(file); - } /* end case */ - break; - - case H5D_CHUNKED: - { - hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */ - - /* Set up layout information */ - if((ndims = H5S_GET_EXTENT_NDIMS(new_dset->shared->space)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "unable to get rank") - new_dset->shared->layout.u.chunk.ndims = (unsigned)ndims + 1; - HDassert((unsigned)(new_dset->shared->layout.u.chunk.ndims) <= NELMTS(new_dset->shared->layout.u.chunk.dim)); - - /* Initialize to no address */ - new_dset->shared->layout.u.chunk.addr = HADDR_UNDEF; - - /* - * Chunked storage allows any type of data space extension, so we - * don't even bother checking. - */ - if(chunk_ndims != (unsigned)ndims) - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space") - if(new_dset->shared->dcpl_cache.efl.nused > 0) - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout") - - /* - * The chunk size of a dimension with a fixed size cannot exceed - * the maximum dimension size - */ - if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, new_dset->shared->layout.u.chunk.dim) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size") - new_dset->shared->layout.u.chunk.dim[new_dset->shared->layout.u.chunk.ndims-1] = H5T_get_size(new_dset->shared->type); - - if(H5S_get_simple_extent_dims(new_dset->shared->space, NULL, max_dim) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions") - for(u = 0; u < new_dset->shared->layout.u.chunk.ndims - 1; u++) - if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < new_dset->shared->layout.u.chunk.dim[u]) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions") - - /* Compute the total size of a chunk */ - for(u = 1, new_dset->shared->layout.u.chunk.size = new_dset->shared->layout.u.chunk.dim[0]; u < new_dset->shared->layout.u.chunk.ndims; u++) - new_dset->shared->layout.u.chunk.size *= new_dset->shared->layout.u.chunk.dim[u]; - - /* Set the I/O functions for this layout type */ - new_dset->shared->io_ops.readvv = H5D_istore_readvv; - new_dset->shared->io_ops.writevv = H5D_istore_writevv; - - /* Initialize the chunk cache for the dataset */ - if(H5D_istore_init(file, new_dset) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize chunk cache") - - /* Indicate that the chunk information was initialized */ - chunk_init = TRUE; - } /* end case */ - break; - - case H5D_COMPACT: - { - hssize_t tmp_size; /* Temporary holder for raw data size */ - hsize_t comp_data_size; - - /* - * Compact dataset is stored in dataset object header message of - * layout. - */ - tmp_size = H5S_GET_EXTENT_NPOINTS(space) * H5T_get_size(new_dset->shared->type); - H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.compact.size, tmp_size, hssize_t, size_t); - - /* Verify data size is smaller than maximum header message size - * (64KB) minus other layout message fields. - */ - comp_data_size = H5O_MESG_MAX_SIZE - H5O_layout_meta_size(file, &(new_dset->shared->layout)); - if(new_dset->shared->layout.u.compact.size > comp_data_size) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size") - - /* Set the I/O functions for this layout type */ - new_dset->shared->io_ops.readvv = H5D_compact_readvv; - new_dset->shared->io_ops.writevv = H5D_compact_writevv; - } /* end case */ - break; - - default: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet") - } /* end switch */ /*lint !e788 All appropriate cases are covered */ - - /* Update the dataset's object header info. */ - if(H5D_update_oh_info(file, dxpl_id, new_dset) != SUCCEED) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache") - - /* Add the dataset to the list of opened objects in the file */ - if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count") - if(H5FO_insert(new_dset->oloc.file, new_dset->oloc.addr, new_dset->shared, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects") - - new_dset->shared->fo_count = 1; - - /* Success */ - ret_value = new_dset; - -done: - if(!ret_value && new_dset && new_dset->shared) { - if(new_dset->shared) { - if(new_dset->shared->layout.type == H5D_CHUNKED && chunk_init) { - if(H5D_istore_dest(new_dset,H5AC_dxpl_id) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy chunk cache") - } /* end if */ - if(new_dset->shared->space) { - if(H5S_close(new_dset->shared->space) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace") - } /* end if */ - if(new_dset->shared->type) { - if(H5I_dec_ref(new_dset->shared->type_id) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype") - } /* end if */ - if(H5F_addr_defined(new_dset->oloc.addr)) { - if(H5O_close(&(new_dset->oloc)) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header") - if(file) { - if(H5O_delete(file, dxpl_id, new_dset->oloc.addr) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTDELETE, NULL, "unable to delete object header") - } /* end if */ - } /* end if */ - if(new_dset->shared->dcpl_id != 0) { - if(H5I_dec_ref(new_dset->shared->dcpl_id) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list") - } /* end if */ - H5FL_FREE(H5D_shared_t, new_dset->shared); - } /* end if */ - new_dset->oloc.file = NULL; - H5FL_FREE(H5D_t, new_dset); - } /* end if */ - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_create() */ - - -/* - *------------------------------------------------------------------------- - * Function: H5D_open - * - * Purpose: Checks if dataset is already open, or opens a dataset for - * access. - * - * Return: Success: Dataset ID - * Failure: FAIL - * - * Programmer: Quincey Koziol - * Friday, December 20, 2002 - * - *------------------------------------------------------------------------- - */ -H5D_t * -H5D_open(const H5G_loc_t *loc, hid_t dxpl_id) -{ - H5D_shared_t *shared_fo = NULL; - H5D_t *dataset = NULL; - H5D_t *ret_value; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_open, NULL) - - /* check args */ - HDassert(loc); - - /* Allocate the dataset structure */ - if(NULL == (dataset = H5FL_CALLOC(H5D_t))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - - /* Shallow copy (take ownership) of the object location object */ - if(H5O_loc_copy(&(dataset->oloc), loc->oloc, H5_COPY_SHALLOW) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy object location") - - /* Shallow copy (take ownership) of the group hier. path */ - if(H5G_name_copy(&(dataset->path), loc->path, H5_COPY_SHALLOW) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy path") - - /* Check if dataset was already open */ - if((shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr)) == NULL) { - /* Clear any errors from H5FO_opened() */ - H5E_clear_stack(NULL); - - /* Open the dataset object */ - if(H5D_open_oid(dataset, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found") - - /* Add the dataset to the list of opened objects in the file */ - if(H5FO_insert(dataset->oloc.file, dataset->oloc.addr, dataset->shared, FALSE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects") - - /* Increment object count for the object in the top file */ - if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count") - - /* We're the first dataset to use the the shared info */ - dataset->shared->fo_count = 1; - } /* end if */ - else { - /* Point to shared info */ - dataset->shared = shared_fo; - - /* Increment # of datasets using shared information */ - shared_fo->fo_count++; - - /* Check if the object has been opened through the top file yet */ - if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) { - /* Open the object through this top file */ - if(H5O_open(&(dataset->oloc)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open object header") - } /* end if */ - - /* Increment object count for the object in the top file */ - if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count") - } /* end else */ - - ret_value = dataset; - -done: - if(ret_value == NULL) { - /* Free the location--casting away const*/ - if(dataset) { - if(shared_fo == NULL) /* Need to free shared fo */ - H5FL_FREE(H5D_shared_t, dataset->shared); - - H5O_loc_free(&(dataset->oloc)); - H5G_name_free(&(dataset->path)); - - H5FL_FREE(H5D_t, dataset); - } - if(shared_fo) - shared_fo->fo_count--; - } /* end if */ - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_open() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_open_oid - * - * Purpose: Opens a dataset for access. - * - * Return: Dataset pointer on success, NULL on failure - * - * Programmer: Quincey Koziol - * Monday, October 12, 1998 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_open_oid(H5D_t *dataset, hid_t dxpl_id) -{ - H5P_genplist_t *plist; /* Property list */ - H5O_pline_t *pline; /* I/O pipeline information */ - H5O_fill_t *fill_prop; /* Pointer to dataset's fill value info */ - unsigned alloc_time_state; /* Allocation time state */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_open_oid) - - /* check args */ - HDassert(dataset); - - /* (Set the 'vl_type' parameter to FALSE since it doesn't matter from here) */ - if(NULL == (dataset->shared = H5D_new(H5P_DATASET_CREATE_DEFAULT, FALSE, FALSE))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") - - /* Open the dataset object */ - if(H5O_open(&(dataset->oloc)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open") - - /* Get the type and space */ - if(NULL == (dataset->shared->type = (H5T_t *)H5O_msg_read(&(dataset->oloc), H5O_DTYPE_ID, NULL, dxpl_id))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load type info from dataset header") - if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc), dxpl_id))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load space info from dataset header") - - /* Get a datatype ID for the dataset's datatype */ - if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") - - /* Get dataset creation property list object */ - if(NULL == (plist = (H5P_genplist_t *)H5I_object(dataset->shared->dcpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") - - /* Get the optional filters message */ - pline = &dataset->shared->dcpl_cache.pline; - if(NULL != H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, pline, dxpl_id)) { - if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, pline) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set pipeline") - } /* end if */ - else - H5E_clear_stack(NULL); - - /* - * Get the raw data layout info. It's actually stored in two locations: - * the storage message of the dataset (dataset->storage) and certain - * values are copied to the dataset create plist so the user can query - * them. - */ - if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id)) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message") - if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->shared->layout.type) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout") - switch(dataset->shared->layout.type) { - case H5D_CONTIGUOUS: - /* Compute the size of the contiguous storage for versions of the - * layout message less than version 3 because versions 1 & 2 would - * truncate the dimension sizes to 32-bits of information. - QAK 5/26/04 - */ - if(dataset->shared->layout.version < 3) { - hssize_t tmp_size; /* Temporary holder for raw data size */ - - tmp_size = H5S_GET_EXTENT_NPOINTS(dataset->shared->space) * H5T_get_size(dataset->shared->type); - H5_ASSIGN_OVERFLOW(dataset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t); - } /* end if */ - - /* Set the I/O functions for this layout type */ - dataset->shared->io_ops.readvv = H5D_contig_readvv; - dataset->shared->io_ops.writevv = H5D_contig_writevv; - - /* Get the sieve buffer size for this dataset */ - dataset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(dataset->oloc.file); - break; - - case H5D_CHUNKED: - /* - * Chunked storage. The creation plist's dimension is one less than - * the chunk dimension because the chunk includes a dimension for the - * individual bytes of the datatype. - */ - { - unsigned chunk_ndims; /* Dimensionality of chunk */ - - chunk_ndims = dataset->shared->layout.u.chunk.ndims - 1; - - if(H5P_set(plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk dimensions") - if(H5P_set(plist, H5D_CRT_CHUNK_SIZE_NAME, dataset->shared->layout.u.chunk.dim) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk size") - - /* Initialize the chunk cache for the dataset */ - if(H5D_istore_init(dataset->oloc.file, dataset) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache") - } - - /* Set the I/O functions for this layout type */ - dataset->shared->io_ops.readvv = H5D_istore_readvv; - dataset->shared->io_ops.writevv = H5D_istore_writevv; - break; - - case H5D_COMPACT: - /* Set the I/O functions for this layout type */ - dataset->shared->io_ops.readvv = H5D_compact_readvv; - dataset->shared->io_ops.writevv = H5D_compact_writevv; - break; - - default: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet") - } /* end switch */ /*lint !e788 All appropriate cases are covered */ - - /* Point at dataset's copy, to cache it for later */ - fill_prop = &dataset->shared->dcpl_cache.fill; - - /* Try to get the new fill value message from the object header */ - if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_NEW_ID, fill_prop, dxpl_id)) { - H5E_clear_stack(NULL); - - /* For backward compatibility, try to retrieve the old fill value message */ - if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_ID, fill_prop, dxpl_id)) { - H5E_clear_stack(NULL); - - /* Set the space allocation time appropriately, based on the type of dataset storage */ - switch(dataset->shared->layout.type) { - case H5D_COMPACT: - fill_prop->alloc_time = H5D_ALLOC_TIME_EARLY; - break; - - case H5D_CONTIGUOUS: - fill_prop->alloc_time = H5D_ALLOC_TIME_LATE; - break; - - case H5D_CHUNKED: - fill_prop->alloc_time = H5D_ALLOC_TIME_INCR; - break; - - default: - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet") - } /* end switch */ /*lint !e788 All appropriate cases are covered */ - } /* end if */ - - /* If "old" fill value size is 0 (undefined), map it to -1 */ - if(fill_prop->size == 0) - fill_prop->size = (size_t)-1; - } /* end if */ - alloc_time_state = 0; - if((dataset->shared->layout.type == H5D_COMPACT && fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) - || (dataset->shared->layout.type == H5D_CONTIGUOUS && fill_prop->alloc_time == H5D_ALLOC_TIME_LATE) - || (dataset->shared->layout.type == H5D_CHUNKED && fill_prop->alloc_time == H5D_ALLOC_TIME_INCR)) - alloc_time_state = 1; - - /* Set revised fill value properties, if they are different from the defaults */ - if(H5P_fill_value_cmp(&H5D_def_dset.dcpl_cache.fill, fill_prop, sizeof(H5O_fill_t))) { - if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set fill value") - if(H5P_set(plist, H5D_CRT_ALLOC_TIME_STATE_NAME, &alloc_time_state) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set allocation time state") - } /* end if */ - - /* Get the external file list message, which might not exist. Space is - * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */ - if((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr)) - || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) { - if(NULL != H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id)) { - if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list") - - /* Override the I/O functions for this layout type */ - dataset->shared->io_ops.readvv = H5D_efl_readvv; - dataset->shared->io_ops.writevv = H5D_efl_writevv; - } /* end if */ - else - H5E_clear_stack(NULL); - } /* end if */ - - /* - * Make sure all storage is properly initialized. - * This is important only for parallel I/O where the space must - * be fully allocated before I/O can happen. - */ - if((H5F_get_intent(dataset->oloc.file) & H5F_ACC_RDWR) - && ((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr)) - || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) - && IS_H5FD_MPI(dataset->oloc.file)) { - if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_OPEN, TRUE, FALSE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage") - } /* end if */ - -done: - if(ret_value < 0) { - if(H5F_addr_defined(dataset->oloc.addr)) { - if(H5O_close(&(dataset->oloc)) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") - } /* end if */ - if(dataset->shared->space) { - if(H5S_close(dataset->shared->space) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") - } /* end if */ - if(dataset->shared->type) { - if(dataset->shared->type_id > 0) { - if(H5I_dec_ref(dataset->shared->type_id) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") - } /* end if */ - else { - if(H5T_close(dataset->shared->type) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") - } /* end else */ - } /* end if */ - } /* end if */ - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_open_oid() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_close - * - * Purpose: Insures that all data has been saved to the file, closes the - * dataset object header, and frees all resources used by the - * descriptor. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Thursday, December 4, 1997 - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_close(H5D_t *dataset) -{ - unsigned free_failed = FALSE; - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_close, FAIL) - - /* check args */ - HDassert(dataset && dataset->oloc.file && dataset->shared); - HDassert(dataset->shared->fo_count >0); - - /* Dump debugging info */ -#ifdef H5D_ISTORE_DEBUG - H5D_istore_stats(dataset, FALSE); -#endif /* H5F_ISTORE_DEBUG */ - - dataset->shared->fo_count--; - if(dataset->shared->fo_count == 0) { - /* Free the data sieve buffer, if it's been allocated */ - if(dataset->shared->cache.contig.sieve_buf) { - HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ - - /* Flush the raw data buffer, if its dirty */ - if(dataset->shared->cache.contig.sieve_dirty) { - /* Write dirty data sieve buffer to file */ - if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, - dataset->shared->cache.contig.sieve_size, H5AC_dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") - - /* Reset sieve buffer dirty flag */ - dataset->shared->cache.contig.sieve_dirty = FALSE; - } /* end if */ - - dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf); - } /* end if */ - - /* Free cached information for each kind of dataset */ - switch(dataset->shared->layout.type) { - case H5D_CONTIGUOUS: - break; - - case H5D_CHUNKED: - /* Flush and destroy chunks in the cache */ - if(H5D_istore_dest(dataset,H5AC_dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache") - break; - - case H5D_COMPACT: - /* Update header message of layout for compact dataset. */ - if(dataset->shared->layout.u.compact.dirty) { - if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), H5AC_dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to update layout message") - dataset->shared->layout.u.compact.dirty = FALSE; - } /* end if */ - - /* Free the buffer for the raw data for compact datasets */ - dataset->shared->layout.u.compact.buf = H5MM_xfree(dataset->shared->layout.u.compact.buf); - break; - - default: - HDassert("not implemented yet" && 0); -#ifdef NDEBUG - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") -#endif /* NDEBUG */ - } /* end switch */ /*lint !e788 All appropriate cases are covered */ - - /* - * Release datatype, dataspace and creation property list -- there isn't - * much we can do if one of these fails, so we just continue. - */ - free_failed = (H5I_dec_ref(dataset->shared->type_id) < 0 || H5S_close(dataset->shared->space) < 0 || - H5I_dec_ref(dataset->shared->dcpl_id) < 0); - - /* Remove the dataset from the list of opened objects in the file */ - if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") - if(H5FO_delete(dataset->oloc.file, H5AC_dxpl_id, dataset->oloc.addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't remove dataset from list of open objects") - - /* Close the dataset object */ - /* (This closes the file, if this is the last object open) */ - if(H5O_close(&(dataset->oloc)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") - - /* - * Free memory. Before freeing the memory set the file pointer to NULL. - * We always check for a null file pointer in other H5D functions to be - * sure we're not accessing an already freed dataset (see the HDassert() - * above). - */ - dataset->oloc.file = NULL; - - H5FL_FREE(H5D_shared_t, dataset->shared); - } /* end if */ - else { - /* Decrement the ref. count for this object in the top file */ - if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") - - /* Check reference count for this object in the top file */ - if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) - if(H5O_close(&(dataset->oloc)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to close") - } /* end else */ - - /* Release the dataset's path info */ - if(H5G_name_free(&(dataset->path)) < 0) - free_failed = TRUE; - - /* Free the dataset's memory structure */ - H5FL_FREE(H5D_t, dataset); - - /* Check if anything failed in the middle... */ - if(free_failed) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free a component of the dataset, but the dataset was freed anyway.") - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_close() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_oloc - * - * Purpose: Returns a pointer to the object location for a dataset. - * - * Return: Success: Ptr to location - * Failure: NULL - * - * Programmer: Robb Matzke - * Friday, April 24, 1998 - * - *------------------------------------------------------------------------- - */ -H5O_loc_t * -H5D_oloc(H5D_t *dataset) -{ - /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_oloc) - - FUNC_LEAVE_NOAPI(dataset ? &(dataset->oloc) : (H5O_loc_t *)NULL) -} /* end H5D_oloc() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_nameof - * - * Purpose: Returns a pointer to the group hier. path for a dataset. - * - * Return: Success: Ptr to entry - * Failure: NULL - * - * Programmer: Quincey Koziol - * Monday, September 12, 2005 - * - *------------------------------------------------------------------------- - */ -H5G_name_t * -H5D_nameof(H5D_t *dataset) -{ - /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_nameof) - - FUNC_LEAVE_NOAPI(dataset ? &(dataset->path) : (H5G_name_t *)NULL) -} /* end H5D_nameof() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_typeof - * - * Purpose: Returns a pointer to the dataset's datatype. The datatype - * is not copied. - * - * Return: Success: Ptr to the dataset's datatype, uncopied. - * - * Failure: NULL - * - * Programmer: Robb Matzke - * Thursday, June 4, 1998 - * - *------------------------------------------------------------------------- - */ -H5T_t * -H5D_typeof(const H5D_t *dset) -{ - /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_typeof) - - HDassert(dset); - HDassert(dset->shared->type); - - FUNC_LEAVE_NOAPI(dset->shared->type) -} /* end H5D_typeof() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_get_file - * - * Purpose: Returns the dataset's file pointer. - * - * Return: Success: Ptr to the dataset's file pointer. - * - * Failure: NULL - * - * Programmer: Quincey Koziol - * Thursday, October 22, 1998 - * - *------------------------------------------------------------------------- - */ -static H5F_t * -H5D_get_file (const H5D_t *dset) -{ - /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_get_file) - - HDassert(dset); - HDassert(dset->oloc.file); - - FUNC_LEAVE_NOAPI(dset->oloc.file) -} /* end H5D_get_file() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_alloc_storage - * - * Purpose: Allocate storage for the raw data of a dataset. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Friday, January 16, 1998 - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc, - hbool_t update_time, hbool_t full_overwrite) -{ - struct H5O_layout_t *layout; /* The dataset's layout information */ - hbool_t must_init_space = FALSE; /* Flag to indicate that space should be initialized */ - hbool_t addr_set = FALSE; /* Flag to indicate that the dataset's storage address was set */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_alloc_storage) - - /* check args */ - HDassert(f); - HDassert(dset); - - /* If the data is stored in external files, don't set an address for the layout - * We assume that external storage is already - * allocated by the caller, or at least will be before I/O is performed. - */ - if(!(H5S_NULL == H5S_GET_EXTENT_TYPE(dset->shared->space) || dset->shared->dcpl_cache.efl.nused > 0)) { - /* Get a pointer to the dataset's layout information */ - layout = &(dset->shared->layout); - - switch(layout->type) { - case H5D_CONTIGUOUS: - if(!H5F_addr_defined(layout->u.contig.addr)) { - /* Reserve space in the file for the entire array */ - if(H5D_contig_create(f, dxpl_id, layout/*out*/) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage") - - /* Indicate that we set the storage addr */ - addr_set = TRUE; - - /* Indicate that we should initialize storage space */ - must_init_space = TRUE; - } /* end if */ - break; - - case H5D_CHUNKED: - if(!H5F_addr_defined(layout->u.chunk.addr)) { - /* Create the root of the B-tree that describes chunked storage */ - if(H5D_istore_create(f, dxpl_id, layout/*out*/) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") - - /* Indicate that we set the storage addr */ - addr_set = TRUE; - - /* Indicate that we should initialize storage space */ - must_init_space = TRUE; - } /* end if */ - - /* If space allocation is set to 'early' and we are extending - * the dataset, indicate that space should be allocated, so the - * B-tree gets expanded. -QAK - */ - if(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY - && time_alloc == H5D_ALLOC_EXTEND) - must_init_space = 1; - break; - - case H5D_COMPACT: - /* Check if space is already allocated */ - if(layout->u.compact.buf==NULL) { - /* Reserve space in layout header message for the entire array. */ - HDassert(layout->u.compact.size > 0); - if(NULL == (layout->u.compact.buf = H5MM_malloc(layout->u.compact.size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset") - if(!full_overwrite) - HDmemset(layout->u.compact.buf, 0, layout->u.compact.size); - layout->u.compact.dirty = TRUE; - - /* Indicate that we set the storage addr */ - addr_set = TRUE; - - /* Indicate that we should initialize storage space */ - must_init_space = TRUE; - } /* end if */ - break; - - default: - HDassert("not implemented yet" && 0); -#ifdef NDEBUG - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") -#endif /* NDEBUG */ - } /* end switch */ /*lint !e788 All appropriate cases are covered */ - - /* Check if we need to initialize the space */ - if(must_init_space) { - if(layout->type == H5D_CHUNKED) { - /* If we are doing incremental allocation and the B-tree got - * created during a H5Dwrite call, don't initialize the storage - * now, wait for the actual writes to each block and let the - * low-level chunking routines handle initialize the fill-values. - * Otherwise, pass along the space initialization call and let - * the low-level chunking routines sort out whether to write - * fill values to the chunks they allocate space for. Yes, - * this is icky. -QAK - */ - if(!(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_INCR && time_alloc == H5D_ALLOC_WRITE)) - if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") - } /* end if */ - else { - H5D_fill_value_t fill_status; /* The fill value status */ - - /* Check the dataset's fill-value status */ - if(H5P_is_fill_value_defined(&dset->shared->dcpl_cache.fill, &fill_status) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") - - /* If we are filling the dataset on allocation or "if set" and - * the fill value _is_ set, do that now */ - if(dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || - (dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) { - if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") - } /* end if */ - } /* end else */ - } /* end if */ - - /* Also update header message for layout with new address, if we - * set the address. (this is improves forward compatibility). - */ - if(time_alloc != H5D_ALLOC_CREATE && addr_set) - if(H5O_msg_write(&dset->oloc, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_time, &dset->shared->layout, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message") - } /* end if */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_alloc_storage() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_init_storage - * - * Purpose: Initialize the data for a new dataset. If a selection is - * defined for SPACE then initialize only that part of the - * dataset. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Monday, October 5, 1998 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) -{ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_init_storage) - - HDassert(dset); - - switch (dset->shared->layout.type) { - case H5D_COMPACT: - /* If we will be immediately overwriting the values, don't bother to clear them */ - if(!full_overwrite) { - /* Fill the compact dataset storage */ - if(H5D_compact_fill(dset, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize compact dataset storage") - } /* end if */ - break; - - case H5D_CONTIGUOUS: - /* Don't write default fill values to external files */ - /* If we will be immediately overwriting the values, don't bother to clear them */ - if((dset->shared->dcpl_cache.efl.nused == 0 || dset->shared->dcpl_cache.fill.buf) && !full_overwrite) - if(H5D_contig_fill(dset, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") - break; - - case H5D_CHUNKED: - /* - * Allocate file space - * for all chunks now and initialize each chunk with the fill value. - */ - if(H5D_istore_allocate(dset, dxpl_id, full_overwrite) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") - break; - - default: - HDassert("not implemented yet" && 0); -#ifdef NDEBUG - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") -#endif /* NDEBUG */ - } /* end switch */ /*lint !e788 All appropriate cases are covered */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_init_storage() */ - - -/*------------------------------------------------------------------------- * Function: H5Dget_storage_size * * Purpose: Returns the amount of storage that is required for the @@ -2514,57 +693,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_get_storage_size - * - * Purpose: Determines how much space has been reserved to store the raw - * data of a dataset. - * - * Return: Success: Number of bytes reserved to hold raw data. - * - * Failure: 0 - * - * Programmer: Robb Matzke - * Wednesday, April 21, 1999 - * - *------------------------------------------------------------------------- - */ -static hsize_t -H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id) -{ - hsize_t ret_value; - - FUNC_ENTER_NOAPI(H5D_get_storage_size, 0) - - switch(dset->shared->layout.type) { - case H5D_CHUNKED: - if(dset->shared->layout.u.chunk.addr == HADDR_UNDEF) - ret_value=0; - else - ret_value = H5D_istore_allocated(dset, dxpl_id); - break; - - case H5D_CONTIGUOUS: - /* Datasets which are not allocated yet are using no space on disk */ - if(dset->shared->layout.u.contig.addr == HADDR_UNDEF) - ret_value=0; - else - ret_value=dset->shared->layout.u.contig.size; - break; - - case H5D_COMPACT: - ret_value = dset->shared->layout.u.compact.size; - break; - - default: - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset type") - } /*lint !e788 All appropriate cases are covered */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} - - -/*------------------------------------------------------------------------- * Function: H5Dget_offset * * Purpose: Returns the address of dataset in file. @@ -2600,63 +728,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_get_offset - * - * Purpose: Private function for H5D_get_offset. Returns the address - * of dataset in file. - * - * Return: Success: the address of dataset - * - * Failure: HADDR_UNDEF - * - * Programmer: Raymond Lu - * November 6, 2002 - * - *------------------------------------------------------------------------- - */ -static haddr_t -H5D_get_offset(const H5D_t *dset) -{ - haddr_t ret_value=HADDR_UNDEF; - haddr_t base_addr; - H5F_t *f; - - FUNC_ENTER_NOAPI(H5D_get_offset, HADDR_UNDEF) - - HDassert(dset); - - switch(dset->shared->layout.type) { - case H5D_CHUNKED: - case H5D_COMPACT: - break; - - case H5D_CONTIGUOUS: - /* If dataspace hasn't been allocated or dataset is stored in - * an external file, the value will be HADDR_UNDEF. */ - f = H5D_get_file(dset); - base_addr = H5F_get_base_addr(f); - - /* If there's user block in file, returns the absolute dataset offset - * from the beginning of file. */ - if(base_addr!=HADDR_UNDEF) - ret_value = dset->shared->layout.u.contig.addr + base_addr; - else - ret_value = dset->shared->layout.u.contig.addr; - break; - - default: - HDassert("not implemented yet" && 0); -#ifdef NDEBUG - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "unknown dataset layout type") -#endif /* NDEBUG */ - } /*lint !e788 All appropriate cases are covered */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} - - -/*------------------------------------------------------------------------- * Function: H5Diterate * * Purpose: This routine iterates over all the elements selected in a memory @@ -2745,41 +816,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_iterate - * - * Purpose: Internal version of H5Diterate() - * - * Return: Returns the return value of the last operator if it was non-zero, - * or zero if all elements were processed. Otherwise returns a - * negative value. - * - * Programmer: Quincey Koziol - * Tuesday, November 22, 2005 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_iterate(void *buf, hid_t type_id, H5S_t *space, H5D_operator_t op, - void *operator_data) -{ - herr_t ret_value; - - FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_iterate) - - /* Check args */ - HDassert(buf); - HDassert(H5I_DATATYPE == H5I_get_type(type_id)); - HDassert(space); - HDassert(H5S_has_extent(space)); - HDassert(op); - - ret_value = H5S_select_iterate(buf, type_id, space, op, operator_data); - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_iterate() */ - - -/*------------------------------------------------------------------------- * Function: H5Dvlen_reclaim * * Purpose: Frees the buffers allocated for storing variable-length data @@ -2827,142 +863,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_vlen_reclaim - * - * Purpose: Frees the buffers allocated for storing variable-length data - * in memory. Only frees the VL data in the selection defined in the - * dataspace. The dataset transfer property list is required to find the - * correct allocation/free methods for the VL data in the buffer. - * - * Return: Non-negative on success, negative on failure - * - * Programmer: Quincey Koziol - * Tuesday, November 22, 2005 - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_vlen_reclaim(hid_t type_id, H5S_t *space, hid_t plist_id, void *buf) -{ - H5T_vlen_alloc_info_t _vl_alloc_info; /* VL allocation info buffer */ - H5T_vlen_alloc_info_t *vl_alloc_info = &_vl_alloc_info; /* VL allocation info */ - herr_t ret_value; - - FUNC_ENTER_NOAPI(H5D_vlen_reclaim, FAIL) - - /* Check args */ - HDassert(H5I_DATATYPE == H5I_get_type(type_id)); - HDassert(space); - HDassert(H5P_isa_class(plist_id, H5P_DATASET_XFER)); - HDassert(buf); - - /* Get the allocation info */ - if(H5T_vlen_get_alloc_info(plist_id,&vl_alloc_info) < 0) - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "unable to retrieve VL allocation info") - - /* Call H5D_iterate with args, etc. */ - ret_value = H5D_iterate(buf, type_id, space ,H5T_vlen_reclaim, vl_alloc_info); - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_vlen_reclaim() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_vlen_get_buf_size_alloc - * - * Purpose: This routine makes certain there is enough space in the temporary - * buffer for the new data to read in. All the VL data read in is actually - * placed in this buffer, overwriting the previous data. Needless to say, - * this data is not actually usable. - * - * Return: Non-negative on success, negative on failure - * - * Programmer: Quincey Koziol - * Tuesday, August 17, 1999 - * - *------------------------------------------------------------------------- - */ -static void * -H5D_vlen_get_buf_size_alloc(size_t size, void *info) -{ - H5D_vlen_bufsize_t *vlen_bufsize=(H5D_vlen_bufsize_t *)info; - void *ret_value; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_vlen_get_buf_size_alloc, NULL) - - /* Get a temporary pointer to space for the VL data */ - if((vlen_bufsize->vl_tbuf=H5FL_BLK_REALLOC(vlen_vl_buf,vlen_bufsize->vl_tbuf,size))!=NULL) - vlen_bufsize->size+=size; - - /* Set return value */ - ret_value=vlen_bufsize->vl_tbuf; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_vlen_get_buf_size_alloc() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_vlen_get_buf_size - * - * Purpose: This routine checks the number of bytes required to store a single - * element from a dataset in memory, creating a selection with just the - * single element selected to read in the element and using a custom memory - * allocator for any VL data encountered. - * The *size value is modified according to how many bytes are - * required to store the element in memory. - * - * Implementation: This routine actually performs the read with a custom - * memory manager which basically just counts the bytes requested and - * uses a temporary memory buffer (through the H5FL API) to make certain - * enough space is available to perform the read. Then the temporary - * buffer is released and the number of bytes allocated is returned. - * Kinda kludgy, but easier than the other method of trying to figure out - * the sizes without actually reading the data in... - QAK - * - * Return: Non-negative on success, negative on failure - * - * Programmer: Quincey Koziol - * Tuesday, August 17, 1999 - * - *------------------------------------------------------------------------- - */ -/* ARGSUSED */ -static herr_t -H5D_vlen_get_buf_size(void UNUSED *elem, hid_t type_id, unsigned UNUSED ndim, const hsize_t *point, void *op_data) -{ - H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)op_data; - H5T_t *dt; /* Datatype for operation */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5D_vlen_get_buf_size) - - HDassert(op_data); - HDassert(H5I_DATATYPE == H5I_get_type(type_id)); - - /* Check args */ - if(NULL == (dt = (H5T_t *)H5I_object(type_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype") - - /* Make certain there is enough fixed-length buffer available */ - if(NULL == (vlen_bufsize->fl_tbuf = H5FL_BLK_REALLOC(vlen_fl_buf, vlen_bufsize->fl_tbuf, H5T_get_size(dt)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't resize tbuf") - - /* Select point to read in */ - if(H5Sselect_elements(vlen_bufsize->fspace_id, H5S_SELECT_SET, (size_t)1, (const hsize_t **)point) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't select point") - - /* Read in the point (with the custom VL memory allocator) */ - if(H5Dread(vlen_bufsize->dataset_id, type_id, vlen_bufsize->mspace_id, vlen_bufsize->fspace_id, vlen_bufsize->xfer_pid, vlen_bufsize->fl_tbuf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point") - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_vlen_get_buf_size() */ - - -/*------------------------------------------------------------------------- * Function: H5Dvlen_get_buf_size * * Purpose: This routine checks the number of bytes required to store the VL @@ -3039,7 +939,7 @@ H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id, HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") /* Set the memory manager to the special allocation routine */ - if(H5P_set_vlen_mem_manager(plist,H5D_vlen_get_buf_size_alloc,&vlen_bufsize,NULL,NULL) < 0) + if(H5P_set_vlen_mem_manager(plist, H5D_vlen_get_buf_size_alloc, &vlen_bufsize, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't set VL data allocation routine") /* Set the initial number of bytes required */ @@ -3110,248 +1010,3 @@ done: FUNC_LEAVE_API(ret_value) } /* end H5Dset_extent() */ - -/*------------------------------------------------------------------------- - * Function: H5D_set_extent - * - * Purpose: Based on H5D_extend, allows change to a lower dimension, - * calls H5S_set_extent and H5D_istore_prune_by_extent instead - * - * Return: Non-negative on success, negative on failure - * - * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu - * April 9, 2002 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) -{ - H5S_t *space; /* Dataset's dataspace */ - int rank; /* Dataspace # of dimensions */ - hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dimension sizes */ - htri_t changed; /* Whether the dataspace changed size */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_set_extent, FAIL) - - /* Check args */ - HDassert(dset); - HDassert(size); - - /*------------------------------------------------------------------------- - * Get the data space - *------------------------------------------------------------------------- - */ - space = dset->shared->space; - - /*------------------------------------------------------------------------- - * Check if we are shrinking or expanding any of the dimensions - *------------------------------------------------------------------------- - */ - if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") - - /*------------------------------------------------------------------------- - * Modify the size of the data space - *------------------------------------------------------------------------- - */ - if((changed = H5S_set_extent(space, size)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") - - /* Don't bother updating things, unless they've changed */ - if(changed) { - hbool_t shrink = FALSE; /* Flag to indicate a dimension has shrank */ - hbool_t expand = FALSE; /* Flag to indicate a dimension has grown */ - unsigned u; /* Local index variable */ - - /* Determine if we are shrinking and/or expanding any dimensions */ - for(u = 0; u < (unsigned)rank; u++) { - if(size[u] < curr_dims[u]) - shrink = TRUE; - if(size[u] > curr_dims[u]) - expand = TRUE; - } /* end for */ - - /*------------------------------------------------------------------------- - * Modify the dataset storage - *------------------------------------------------------------------------- - */ - /* Save the new dataspace in the file if necessary */ - if(H5S_write(&(dset->oloc), space, TRUE, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") - - /* Update the index values for the cached chunks for this dataset */ - if(H5D_CHUNKED == dset->shared->layout.type) - if(H5D_istore_update_cache(dset, dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices") - - /* Allocate space for the new parts of the dataset, if appropriate */ - if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY) - if(H5D_alloc_storage(dset->oloc.file, dxpl_id, dset, H5D_ALLOC_EXTEND, TRUE, FALSE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage") - - - /*------------------------------------------------------------------------- - * Remove chunk information in the case of chunked datasets - * This removal takes place only in case we are shrinking the dateset - *------------------------------------------------------------------------- - */ - if(shrink && H5D_CHUNKED == dset->shared->layout.type) { - H5D_io_info_t io_info; /* Dataset I/O info */ - H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ - H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ - - /* Fill the DXPL cache values for later use */ - if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") - - /* Construct dataset I/O info */ - H5D_BUILD_IO_INFO(&io_info, dset, dxpl_cache, dxpl_id, NULL); - - /* Remove excess chunks */ - if(H5D_istore_prune_by_extent(&io_info, curr_dims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ") - - /* Reset the elements outsize the new dimensions, but in existing chunks */ - if(H5D_istore_initialize_by_extent(&io_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks ") - } /* end if */ - } /* end if */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_set_extent() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_flush - * - * Purpose: Flush any dataset information cached in memory - * - * Return: Success: Non-negative - * Failure: Negative - * - * Programmer: Ray Lu - * August 14, 2002 - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_flush(const H5F_t *f, hid_t dxpl_id, unsigned flags) -{ - hid_t *id_list = NULL; /* Array of dataset IDs */ - unsigned num_dsets; /* Number of datasets in file */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_flush, FAIL) - - /* Check args */ - HDassert(f); - - /* Retrieve the # of outstanding dataset IDs */ - num_dsets = H5F_get_obj_count(f, H5F_OBJ_DATASET); - - /* Check for something to do */ - if(num_dsets > 0) { - H5D_t *dataset; /* Dataset pointer */ - unsigned u; /* Index variable */ - - H5_CHECK_OVERFLOW(num_dsets, unsigned, size_t); - if(NULL == (id_list = (hid_t *)H5MM_malloc((size_t)num_dsets * sizeof(hid_t)))) - HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to allocate memory for ID list") - if(H5F_get_obj_ids(f, H5F_OBJ_DATASET, -1, id_list) != num_dsets) - HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset ID list") - - /* Iterate through the open datasets */ - for(u = 0; u < num_dsets; u++) { - if(NULL == (dataset = (H5D_t *)H5I_object_verify(id_list[u], H5I_DATASET))) - HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset object") - - /* Flush the raw data buffer, if we have a dirty one */ - if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) { - HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ - - /* Write dirty data sieve buffer to file */ - if(H5F_block_write(f, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, - dataset->shared->cache.contig.sieve_size, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") - - /* Reset sieve buffer dirty flag */ - dataset->shared->cache.contig.sieve_dirty = FALSE; - } /* end if */ - - /* Flush cached information for each kind of dataset */ - switch(dataset->shared->layout.type) { - case H5D_CONTIGUOUS: - break; - - case H5D_CHUNKED: - /* Flush the raw data cache */ - if(H5D_istore_flush(dataset, dxpl_id, flags & H5F_FLUSH_INVALIDATE) < 0) - HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush raw data cache") - break; - - case H5D_COMPACT: - if(dataset->shared->layout.u.compact.dirty) { - if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), dxpl_id) < 0) - HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") - dataset->shared->layout.u.compact.dirty = FALSE; - } /* end if */ - break; - - default: - HDassert("not implemented yet" && 0); -#ifdef NDEBUG - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") -#endif /* NDEBUG */ - } /* end switch */ /*lint !e788 All appropriate cases are covered */ - } /* end for */ - } /* end if */ - -done: - if(id_list) - H5MM_xfree(id_list); - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D_flush() */ - - -/*------------------------------------------------------------------------- - * Function: H5Ddebug - * - * Purpose: Prints various information about a dataset. This function is - * not to be documented in the API at this time. - * - * Return: Success: Non-negative - * - * Failure: Negative - * - * Programmer: Robb Matzke - * Wednesday, April 28, 1999 - * - *------------------------------------------------------------------------- - */ -herr_t -H5Ddebug(hid_t dset_id) -{ - H5D_t *dset; /* Dataset to debug */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_API(H5Ddebug, FAIL) - H5TRACE1("e", "i", dset_id); - - /* Check args */ - if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") - - /* Print B-tree information */ - if(H5D_CHUNKED == dset->shared->layout.type) - (void)H5D_istore_dump_btree(dset->oloc.file, H5AC_dxpl_id, stdout, dset->shared->layout.u.chunk.ndims, dset->shared->layout.u.chunk.addr); - else if(H5D_CONTIGUOUS == dset->shared->layout.type) - HDfprintf(stdout, " %-10s %a\n", "Address:", dset->shared->layout.u.contig.addr); - -done: - FUNC_LEAVE_API(ret_value) -} /* end H5Ddebug() */ - diff --git a/src/H5Ddbg.c b/src/H5Ddbg.c new file mode 100644 index 0000000..4ca5b21 --- /dev/null +++ b/src/H5Ddbg.c @@ -0,0 +1,123 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/****************/ +/* Module Setup */ +/****************/ + +#define H5D_PACKAGE /*suppress error about including H5Dpkg */ + +/* Interface initialization */ +#define H5_INTERFACE_INIT_FUNC H5D_init_dbg_interface + + +/***********/ +/* Headers */ +/***********/ +#include "H5private.h" /* Generic Functions */ +#include "H5Dpkg.h" /* Datasets */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5Iprivate.h" /* IDs */ + + +/****************/ +/* Local Macros */ +/****************/ + + +/******************/ +/* Local Typedefs */ +/******************/ + + +/********************/ +/* Local Prototypes */ +/********************/ + + +/*********************/ +/* Package Variables */ +/*********************/ + + +/*****************************/ +/* Library Private Variables */ +/*****************************/ + + +/*******************/ +/* Local Variables */ +/*******************/ + + +/*-------------------------------------------------------------------------- +NAME + H5D_init_dbg_interface -- Initialize interface-specific information +USAGE + herr_t H5D_init_dbg_interface() +RETURNS + Non-negative on success/Negative on failure +DESCRIPTION + Initializes any interface-specific data or routines. (Just calls + H5D_init() currently). + +--------------------------------------------------------------------------*/ +static herr_t +H5D_init_dbg_interface(void) +{ + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_init_dbg_interface) + + FUNC_LEAVE_NOAPI(H5D_init()) +} /* H5D_init_dbg_interface() */ + + +/*------------------------------------------------------------------------- + * Function: H5Ddebug + * + * Purpose: Prints various information about a dataset. This function is + * not to be documented in the API at this time. + * + * Return: Success: Non-negative + * + * Failure: Negative + * + * Programmer: Robb Matzke + * Wednesday, April 28, 1999 + * + *------------------------------------------------------------------------- + */ +herr_t +H5Ddebug(hid_t dset_id) +{ + H5D_t *dset; /* Dataset to debug */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_API(H5Ddebug, FAIL) + H5TRACE1("e", "i", dset_id); + + /* Check args */ + if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + + /* Print B-tree information */ + if(H5D_CHUNKED == dset->shared->layout.type) + (void)H5D_istore_dump_btree(dset->oloc.file, H5AC_dxpl_id, stdout, dset->shared->layout.u.chunk.ndims, dset->shared->layout.u.chunk.addr); + else if(H5D_CONTIGUOUS == dset->shared->layout.type) + HDfprintf(stdout, " %-10s %a\n", "Address:", dset->shared->layout.u.contig.addr); + +done: + FUNC_LEAVE_API(ret_value) +} /* end H5Ddebug() */ + diff --git a/src/H5Ddeprec.c b/src/H5Ddeprec.c index d23df69..95f89cf 100644 --- a/src/H5Ddeprec.c +++ b/src/H5Ddeprec.c @@ -327,30 +327,9 @@ H5D_extend(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id) HDassert(dataset); HDassert(size); - /* Check if the filters in the DCPL will need to encode, and if so, can they? - * Filters need encoding if fill value is defined and a fill policy is set that requires - * writing on an extend. - */ - fill = &dataset->shared->dcpl_cache.fill; - if(!dataset->shared->checked_filters) { - H5D_fill_value_t fill_status; /* Whether the fill value is defined */ - - /* Retrieve the "defined" status of the fill value */ - if(H5P_is_fill_value_defined(fill, &fill_status) < 0) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Couldn't retrieve fill value from dataset.") - - /* See if we can check the filter status */ - if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) { - if(fill->fill_time == H5D_FILL_TIME_ALLOC || - (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) { - /* Filters must have encoding enabled. Ensure that all filters can be applied */ - if(H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0) - HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters") - - dataset->shared->checked_filters = TRUE; - } /* end if */ - } /* end if */ - } /* end if */ + /* Check if the filters in the DCPL will need to encode, and if so, can they? */ + if(H5D_check_filters(dataset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't apply filters") /* * NOTE: Restrictions on extensions were checked when the dataset was @@ -375,6 +354,7 @@ H5D_extend(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices") /* Allocate space for the new parts of the dataset, if appropriate */ + fill = &dataset->shared->dcpl_cache.fill; if(fill->alloc_time == H5D_ALLOC_TIME_EARLY) if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_EXTEND, TRUE, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") diff --git a/src/H5Dfill.c b/src/H5Dfill.c index 2d52713..bfb4354 100644 --- a/src/H5Dfill.c +++ b/src/H5Dfill.c @@ -290,7 +290,7 @@ H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, /* Convert disk buffer into memory buffer */ if(!H5T_path_noop(tpath)) { void *elem_ptr; /* Pointer to element to use for fill value */ - void *bkg_ptr; /* Pointer to background element to use for fill value */ + void *bkg_ptr = NULL; /* Pointer to background element to use for fill value */ /* Wrap the local buffer for elements */ if(NULL == (elem_wb = H5WB_wrap(elem_buf, sizeof(elem_buf)))) diff --git a/src/H5Dint.c b/src/H5Dint.c new file mode 100644 index 0000000..5584187 --- /dev/null +++ b/src/H5Dint.c @@ -0,0 +1,2425 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/****************/ +/* Module Setup */ +/****************/ + +#define H5D_PACKAGE /*suppress error about including H5Dpkg */ + +/* Interface initialization */ +#define H5_INTERFACE_INIT_FUNC H5D_init_interface + + +/***********/ +/* Headers */ +/***********/ +#include "H5private.h" /* Generic Functions */ +#include "H5Dpkg.h" /* Datasets */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5FOprivate.h" /* File objects */ +#include "H5HLprivate.h" /* Local heaps */ +#include "H5Iprivate.h" /* IDs */ +#include "H5Lprivate.h" /* Links */ +#include "H5MMprivate.h" /* Memory management */ + + +/****************/ +/* Local Macros */ +/****************/ + + +/******************/ +/* Local Typedefs */ +/******************/ + + +/********************/ +/* Local Prototypes */ +/********************/ + +/* General stuff */ +static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite, hid_t dxpl_id); +static H5D_shared_t *H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type); +static herr_t H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, + const H5T_t *type); +static herr_t H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space); +static herr_t H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset); +static herr_t H5D_open_oid(H5D_t *dataset, hid_t dxpl_id); + + +/*********************/ +/* Package Variables */ +/*********************/ + +/* Define a "default" dataset transfer property list cache structure to use for default DXPLs */ +H5D_dxpl_cache_t H5D_def_dxpl_cache; + +/* Declare a free list to manage blocks of VL data */ +H5FL_BLK_DEFINE(vlen_vl_buf); + +/* Declare a free list to manage other blocks of VL data */ +H5FL_BLK_DEFINE(vlen_fl_buf); + + +/*****************************/ +/* Library Private Variables */ +/*****************************/ + + +/*******************/ +/* Local Variables */ +/*******************/ + +/* Declare a free list to manage the H5D_t and H5D_shared_t structs */ +H5FL_DEFINE_STATIC(H5D_t); +H5FL_DEFINE_STATIC(H5D_shared_t); + +/* Declare the external PQ free list for the sieve buffer information */ +H5FL_BLK_EXTERN(sieve_buf); + +/* Define a static "default" dataset structure to use to initialize new datasets */ +static H5D_shared_t H5D_def_dset; + + + +/*------------------------------------------------------------------------- + * Function: H5D_init + * + * Purpose: Initialize the interface from some other layer. + * + * Return: Success: non-negative + * + * Failure: negative + * + * Programmer: Quincey Koziol + * Saturday, March 4, 2000 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_init(void) +{ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5D_init, FAIL) + /* FUNC_ENTER() does all the work */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_init() */ + + +/*-------------------------------------------------------------------------- +NAME + H5D_init_interface -- Initialize interface-specific information +USAGE + herr_t H5D_init_interface() + +RETURNS + Non-negative on success/Negative on failure +DESCRIPTION + Initializes any interface-specific data or routines. +NOTES + Care must be taken when using the H5P functions, since they can cause + a deadlock in the library when the library is attempting to terminate -QAK + +--------------------------------------------------------------------------*/ +static herr_t +H5D_init_interface(void) +{ + H5P_genplist_t *def_dcpl; /* Default Dataset Creation Property list */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_init_interface) + + /* Initialize the atom group for the dataset IDs */ + if(H5I_register_type(H5I_DATASET, (size_t)H5I_DATASETID_HASHSIZE, H5D_RESERVED_ATOMS, (H5I_free_t)H5D_close)<H5I_FILE) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize interface") + + /* Reset the "default dataset" information */ + HDmemset(&H5D_def_dset, 0, sizeof(H5D_shared_t)); + + /* Get the default dataset creation property list values and initialize the + * default dataset with them. + */ + if(NULL == (def_dcpl = (H5P_genplist_t *)H5I_object(H5P_LST_DATASET_CREATE_g))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "can't get default dataset creation property list") + + /* Get the default data storage method */ + if(H5P_get(def_dcpl, H5D_CRT_LAYOUT_NAME, &H5D_def_dset.layout.type) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve layout") + + /* Get the default dataset creation properties */ + if(H5P_get(def_dcpl, H5D_CRT_EXT_FILE_LIST_NAME, &H5D_def_dset.dcpl_cache.efl) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve external file list") + if(H5P_get(def_dcpl, H5D_CRT_FILL_VALUE_NAME, &H5D_def_dset.dcpl_cache.fill) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill value") + if(H5P_get(def_dcpl, H5D_CRT_DATA_PIPELINE_NAME, &H5D_def_dset.dcpl_cache.pline) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve pipeline filter") + + /* Reset the "default DXPL cache" information */ + HDmemset(&H5D_def_dxpl_cache, 0, sizeof(H5D_dxpl_cache_t)); + + /* Get the default DXPL cache information */ + if(H5D_get_dxpl_cache_real(H5P_DATASET_XFER_DEFAULT, &H5D_def_dxpl_cache) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve default DXPL info") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_init_interface() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_term_interface + * + * Purpose: Terminate this interface. + * + * Return: Success: Positive if anything was done that might + * affect other interfaces; zero otherwise. + * + * Failure: Negative. + * + * Programmer: Robb Matzke + * Friday, November 20, 1998 + * + *------------------------------------------------------------------------- + */ +int +H5D_term_interface(void) +{ + int n=0; + + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_term_interface) + + if(H5_interface_initialize_g) { + if((n=H5I_nmembers(H5I_DATASET))>0) { + /* The dataset API uses the "force" flag set to true because it + * is using the "file objects" (H5FO) API functions to track open + * objects in the file. Using the H5FO code means that dataset + * IDs can have reference counts >1, when an existing dataset is + * opened more than once. However, the H5I code does not attempt + * to close objects with reference counts>1 unless the "force" flag + * is set to true. + * + * At some point (probably after the group and datatypes use the + * the H5FO code), the H5FO code might need to be switched around + * to storing pointers to the objects being tracked (H5D_t, H5G_t, + * etc) and reference count those itself instead of relying on the + * reference counting in the H5I layer. Then, the "force" flag can + * be put back to false. + * + * Setting the "force" flag to true for all the interfaces won't + * work because the "file driver" (H5FD) APIs use the H5I reference + * counting to avoid closing a file driver out from underneath an + * open file... + * + * QAK - 5/13/03 + */ + H5I_clear_type(H5I_DATASET, TRUE); + } else { + H5I_dec_type_ref(H5I_DATASET); + H5_interface_initialize_g = 0; + n = 1; /*H5I*/ + } + } + FUNC_LEAVE_NOAPI(n) +} /* end H5D_term_interface() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_create_named + * + * Purpose: Internal routine to create a new dataset. + * + * Return: Success: Non-NULL, pointer to new dataset object. + * + * Failure: NULL + * + * Programmer: Quincey Koziol + * Thursday, April 5, 2007 + * + *------------------------------------------------------------------------- + */ +H5D_t * +H5D_create_named(const H5G_loc_t *loc, const char *name, hid_t type_id, + const H5S_t *space, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id, + hid_t dxpl_id) +{ + H5O_obj_create_t ocrt_info; /* Information for object creation */ + H5D_obj_create_t dcrt_info; /* Information for dataset creation */ + H5D_t *ret_value; /* Return value */ + + FUNC_ENTER_NOAPI(H5D_create_named, NULL) + + /* Check arguments */ + HDassert(loc); + HDassert(name && *name); + HDassert(type_id != H5P_DEFAULT); + HDassert(space); + HDassert(lcpl_id != H5P_DEFAULT); + HDassert(dcpl_id != H5P_DEFAULT); + HDassert(dapl_id != H5P_DEFAULT); + HDassert(dxpl_id != H5P_DEFAULT); + + /* Set up dataset creation info */ + dcrt_info.type_id = type_id; + dcrt_info.space = space; + dcrt_info.dcpl_id = dcpl_id; + + /* Set up object creation information */ + ocrt_info.obj_type = H5O_TYPE_DATASET; + ocrt_info.crt_info = &dcrt_info; + ocrt_info.new_obj = NULL; + + /* Create the new dataset and link it to its parent group */ + if(H5L_link_object(loc, name, &ocrt_info, lcpl_id, dapl_id, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to create and link to dataset") + HDassert(ocrt_info.new_obj); + + /* Set the return value */ + ret_value = (H5D_t *)ocrt_info.new_obj; + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_create_named() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_get_space_status + * + * Purpose: Returns the status of data space allocation. + * + * Return: + * Success: Non-negative + * + * Failture: Negative + * + * Programmer: Raymond Lu + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id) +{ + H5S_t *space; /* Dataset's dataspace */ + hsize_t space_allocated; /* The number of bytes allocated for chunks */ + hssize_t total_elem; /* The total number of elements in dataspace */ + size_t type_size; /* The size of the datatype for the dataset */ + hsize_t full_size; /* The number of bytes in the dataset when fully populated */ + herr_t ret_value = SUCCEED; + + FUNC_ENTER_NOAPI_NOINIT(H5D_get_space_status) + + HDassert(dset); + + /* Get the dataset's dataspace */ + space = dset->shared->space; + HDassert(space); + + /* Get the total number of elements in dataset's dataspace */ + if((total_elem=H5S_GET_EXTENT_NPOINTS(space)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get # of dataspace elements") + + /* Get the size of the dataset's datatype */ + if((type_size = H5T_get_size(dset->shared->type)) == 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get size of datatype") + + /* Compute the maximum size of the dataset in bytes */ + H5_CHECK_OVERFLOW(total_elem,hssize_t,hsize_t); + full_size=((hsize_t)total_elem)*type_size; + + /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */ + space_allocated = H5D_get_storage_size(dset, dxpl_id); + + /* Decide on how much of the space is allocated */ + if(space_allocated == 0) + *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED; + else if(space_allocated == full_size) + *allocation = H5D_SPACE_STATUS_ALLOCATED; + else { + /* Should only happen for chunked datasets currently */ + HDassert(dset->shared->layout.type == H5D_CHUNKED); + + *allocation = H5D_SPACE_STATUS_PART_ALLOCATED; + } /* end else */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_get_space_status() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_new + * + * Purpose: Creates a new, empty dataset structure + * + * Return: Success: Pointer to a new dataset descriptor. + * + * Failure: NULL + * + * Programmer: Quincey Koziol + * Monday, October 12, 1998 + * + *------------------------------------------------------------------------- + */ +static H5D_shared_t * +H5D_new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type) +{ + H5P_genplist_t *plist; /* Property list created */ + H5D_shared_t *new_dset = NULL; /* New dataset object */ + H5D_shared_t *ret_value; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_new) + + /* Allocate new shared dataset structure */ + if(NULL == (new_dset = H5FL_MALLOC(H5D_shared_t))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + + /* Copy the default dataset information */ + HDmemcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t)); + + /* If we are using the default dataset creation property list, during creation + * don't bother to copy it, just increment the reference count + */ + if(!vl_type && creating && dcpl_id == H5P_DATASET_CREATE_DEFAULT) { + if(H5I_inc_ref(dcpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "Can't increment default DCPL ID") + new_dset->dcpl_id = dcpl_id; + } /* end if */ + else { + /* Get the property list */ + if(NULL == (plist = (H5P_genplist_t *)H5I_object(dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list") + + new_dset->dcpl_id = H5P_copy_plist(plist); + } /* end else */ + + /* Set return value */ + ret_value = new_dset; + +done: + if(ret_value == NULL) + if(new_dset != NULL) { + if(new_dset->dcpl_id != 0) + (void)H5I_dec_ref(new_dset->dcpl_id); + H5FL_FREE(H5D_shared_t, new_dset); + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_new() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_init_type + * + * Purpose: Copy a datatype for a dataset's use, performing all the + * necessary adjustments, etc. + * + * Return: Success: SUCCEED + * Failure: FAIL + * + * Programmer: Quincey Koziol + * Thursday, June 24, 2004 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_init_type(H5F_t *file, const H5D_t *dset, hid_t type_id, const H5T_t *type) +{ + htri_t relocatable; /* Flag whether the type is relocatable */ + htri_t immutable; /* Flag whether the type is immutable */ + hbool_t use_latest_format; /* Flag indicating the newest file format should be used */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_init_type) + + /* Sanity checking */ + HDassert(file); + HDassert(dset); + HDassert(type); + + /* Check whether the datatype is relocatable */ + if((relocatable = H5T_is_relocatable(type)) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?") + + /* Check whether the datatype is immutable */ + if((immutable = H5T_is_immutable(type)) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "can't check datatype?") + + /* Get the file's 'use the latest version of the format' flag */ + use_latest_format = H5F_USE_LATEST_FORMAT(file); + + /* Copy the datatype if it's a custom datatype or if it'll change when it's location is changed */ + if(!immutable || relocatable || use_latest_format) { + /* Copy datatype for dataset */ + if((dset->shared->type = H5T_copy(type, H5T_COPY_ALL)) == NULL) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy datatype") + + /* Mark any datatypes as being on disk now */ + if(H5T_set_loc(dset->shared->type, file, H5T_LOC_DISK) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't set datatype location") + + /* Set the latest format, if requested */ + if(use_latest_format) + if(H5T_set_latest_version(dset->shared->type) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype") + + /* Get a datatype ID for the dataset's datatype */ + if((dset->shared->type_id = H5I_register(H5I_DATATYPE, dset->shared->type)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") + } /* end if */ + /* Not a custom datatype, just use it directly */ + else { + if(H5I_inc_ref(type_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment datatype ID") + + /* Use existing datatype */ + dset->shared->type_id = type_id; + dset->shared->type = (H5T_t *)type; /* (Cast away const OK - QAK) */ + } /* end else */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_init_type() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_init_space + * + * Purpose: Copy a dataspace for a dataset's use, performing all the + * necessary adjustments, etc. + * + * Return: Success: SUCCEED + * Failure: FAIL + * + * Programmer: Quincey Koziol + * Tuesday, July 24, 2007 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space) +{ + hbool_t use_latest_format; /* Flag indicating the newest file format should be used */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_init_space) + + /* Sanity checking */ + HDassert(file); + HDassert(dset); + HDassert(space); + + /* Get the file's 'use the latest version of the format' flag */ + use_latest_format = H5F_USE_LATEST_FORMAT(file); + + /* Copy dataspace for dataset */ + if(NULL == (dset->shared->space = H5S_copy(space, FALSE))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy dataspace") + + /* Set the latest format, if requested */ + if(use_latest_format) + if(H5S_set_latest_version(dset->shared->space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set latest version of datatype") + + /* Set the dataset's dataspace to 'all' selection */ + if(H5S_select_all(dset->shared->space, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set all selection") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_init_space() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_update_oh_info + * + * Purpose: Create and fill object header for dataset + * + * Return: Success: SUCCEED + * Failure: FAIL + * + * Programmer: Bill Wendling + * Thursday, October 31, 2002 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset) +{ + struct H5O_t *oh = NULL; /* Pointer to dataset's object header */ + size_t ohdr_size = H5D_MINHDR_SIZE; /* Size of dataset's object header */ + H5O_loc_t *oloc = NULL; /* Dataset's object location */ + H5O_layout_t *layout; /* Dataset's layout information */ + H5T_t *type; /* Dataset's datatype */ + hbool_t use_latest_format; /* Flag indicating the newest file format should be used */ + H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ + H5D_fill_value_t fill_status; /* Fill value status */ + hbool_t fill_changed = FALSE; /* Flag indicating the fill value was changed */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_update_oh_info) + + /* Sanity checking */ + HDassert(file); + HDassert(dset); + + /* Set some local variables, for convenience */ + oloc = &dset->oloc; + layout = &dset->shared->layout; + type = dset->shared->type; + fill_prop = &dset->shared->dcpl_cache.fill; + + /* Get the file's 'use the latest version of the format' flag */ + use_latest_format = H5F_USE_LATEST_FORMAT(file); + + /* Retrieve "defined" status of fill value */ + if(H5P_is_fill_value_defined(fill_prop, &fill_status) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") + + /* Special case handling for variable-length types */ + if(H5T_detect_class(type, H5T_VLEN)) { + /* If the default fill value is chosen for variable-length types, always write it */ + if(fill_prop->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_DEFAULT) { + /* Update dataset creation property */ + fill_prop->fill_time = H5D_FILL_TIME_ALLOC; + + /* Note that the fill value changed */ + fill_changed = TRUE; + } /* end if */ + + /* Don't allow never writing fill values with variable-length types */ + if(fill_prop->fill_time == H5D_FILL_TIME_NEVER) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Dataset doesn't support VL datatype when fill value is not defined") + } /* end if */ + + /* Determine whether fill value is defined or not */ + if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) { + /* Convert fill value buffer to dataset's datatype */ + if(fill_prop->buf && fill_prop->size > 0 && H5O_fill_convert(fill_prop, type, &fill_changed, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert fill value to dataset type") + + fill_prop->fill_defined = TRUE; + } else if(fill_status == H5D_FILL_VALUE_UNDEFINED) { + fill_prop->fill_defined = FALSE; + } else + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine if fill value is defined") + + /* Check for invalid fill & allocation time setting */ + if(fill_prop->fill_defined == FALSE && fill_prop->fill_time == H5D_FILL_TIME_ALLOC) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "fill value writing on allocation set, but no fill value defined") + + /* Check if the fill value info changed */ + if(fill_changed) { + H5P_genplist_t *dc_plist; /* Dataset's creation property list */ + + /* Get dataset's property list object */ + HDassert(dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT); + if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") + + /* Update dataset creation property */ + if(H5P_set(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value info") + } /* end if */ + + /* Add the dataset's raw data size to the size of the header, if the raw data will be stored as compact */ + if(layout->type == H5D_COMPACT) + ohdr_size += layout->u.compact.size; + + /* Create an object header for the dataset */ + if(H5O_create(file, dxpl_id, ohdr_size, dset->shared->dcpl_id, oloc/*out*/) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset object header") + + /* Get a pointer to the object header itself */ + if((oh = H5O_protect(oloc, dxpl_id)) == NULL) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to protect dataset object header") + + /* Write new fill value message */ + if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_NEW_ID, H5O_MSG_FLAG_CONSTANT, 0, fill_prop) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update new fill value header message") + + /* If there is valid information for the old fill value struct, add it */ + /* (only if we aren't trying to write the latest version of the file format) */ + if(fill_prop->buf && !use_latest_format) { + H5O_fill_t old_fill_prop; /* Copy of fill value property, for writing as "old" fill value */ + + /* Shallow copy the fill value property */ + /* (we only want to make certain that the shared component isnt' modified) */ + HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop)); + + /* Reset shared component info */ + H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop); + + /* Write old fill value */ + if(H5O_msg_append(file, dxpl_id, oh, H5O_FILL_ID, H5O_MSG_FLAG_CONSTANT, 0, &old_fill_prop) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update old fill value header message") + } /* end if */ + + /* Update the datatype and dataspace header messages */ + if(H5O_msg_append(file, dxpl_id, oh, H5O_DTYPE_ID, H5O_MSG_FLAG_CONSTANT, 0, type) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update datatype header message") + if(H5S_append(file, dxpl_id, oh, dset->shared->space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update dataspace header message") + + /* Update the filters message, if this is a chunked dataset */ + if(layout->type == H5D_CHUNKED) { + H5O_pline_t *pline; /* Dataset's I/O pipeline information */ + + pline = &dset->shared->dcpl_cache.pline; + if(pline->nused > 0 && H5O_msg_append(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message") + } /* end if */ + + /* + * Allocate storage if space allocate time is early; otherwise delay + * allocation until later. + */ + if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) + if(H5D_alloc_storage(file, dxpl_id, dset, H5D_ALLOC_CREATE, FALSE, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") + + /* Update external storage message, if it's used */ + if(dset->shared->dcpl_cache.efl.nused > 0) { + H5O_efl_t *efl = &dset->shared->dcpl_cache.efl; /* Dataset's external file list */ + H5HL_t *heap; /* Pointer to local heap for EFL file names */ + size_t heap_size = H5HL_ALIGN(1); + size_t u; + + /* Determine size of heap needed to stored the file names */ + for(u = 0; u < efl->nused; ++u) + heap_size += H5HL_ALIGN(HDstrlen(efl->slot[u].name) + 1); + + /* Create the heap for the EFL file names */ + if(H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr/*out*/) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create EFL file name heap") + + /* Pin the heap down in memory */ + if(NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC_WRITE))) + HGOTO_ERROR(H5E_DATASET, H5E_PROTECT, FAIL, "unable to protect EFL file name heap") + + /* Insert "empty" name first */ + if((size_t)(-1) == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) { + H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr); + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap") + } /* end if */ + + for(u = 0; u < efl->nused; ++u) { + size_t offset; /* Offset of file name in heap */ + + /* Insert file name into heap */ + if((size_t)(-1) == (offset = H5HL_insert(file, dxpl_id, heap, + HDstrlen(efl->slot[u].name) + 1, efl->slot[u].name))) { + H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr); + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap") + } /* end if */ + + /* Store EFL file name offset */ + HDassert(0 == efl->slot[u].name_offset); + efl->slot[u].name_offset = offset; + } /* end for */ + + /* Release the heap */ + if(H5HL_unprotect(file, dxpl_id, heap, efl->heap_addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_PROTECT, FAIL, "unable to unprotect EFL file name heap") + heap = NULL; + + /* Insert EFL message into dataset object header */ + if(H5O_msg_append(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message") + } /* end if */ + + /* Create layout message */ + /* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */ + /* (Note: this is relying on H5D_alloc_storage not calling H5O_msg_write during dataset creation) */ + if(H5O_msg_append(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout") + +#ifdef H5O_ENABLE_BOGUS +{ + H5P_genplist_t *dc_plist; /* Dataset's creation property list */ + + /* Get dataset's property list object */ + if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(dset->shared->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") + + /* Check whether to add a "bogus" message */ + if(H5P_exist_plist(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME) > 0) { + uint8_t bogus_flags = 0; /* Flags for creating "bogus" message */ + + /* Retrieve "bogus" message flags */ + if(H5P_get(dc_plist, H5O_BOGUS_MSG_FLAGS_NAME, &bogus_flags) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get bogus message options") + + /* Add a "bogus" message (for error testing). */ + if(H5O_bogus_oh(file, dxpl_id, oh, (unsigned)bogus_flags) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create 'bogus' message") + } /* end if */ +} +#endif /* H5O_ENABLE_BOGUS */ + + /* Add a modification time message. */ + if(H5O_touch_oh(file, dxpl_id, oh, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time message") + +done: + /* Release pointer to object header itself */ + if(oloc != NULL && oh != NULL) + if(H5O_unprotect(oloc, oh) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to unprotect dataset object header") + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_update_oh_info() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_create + * + * Purpose: Creates a new dataset with name NAME in file F and associates + * with it a datatype TYPE for each element as stored in the + * file, dimensionality information or dataspace SPACE, and + * other miscellaneous properties CREATE_PARMS. All arguments + * are deep-copied before being associated with the new dataset, + * so the caller is free to subsequently modify them without + * affecting the dataset. + * + * Return: Success: Pointer to a new dataset + * + * Failure: NULL + * + * Programmer: Robb Matzke + * Thursday, December 4, 1997 + * + *------------------------------------------------------------------------- + */ +H5D_t * +H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id, + hid_t dxpl_id) +{ + const H5T_t *type; /* Datatype for dataset */ + H5D_t *new_dset = NULL; + int i, ndims; + unsigned chunk_ndims = 0; /* Dimensionality of chunk */ + H5P_genplist_t *dc_plist = NULL; /* New Property list */ + hbool_t has_vl_type = FALSE; /* Flag to indicate a VL-type for dataset */ + hbool_t chunk_init = FALSE; /* Flag to indicate that chunk information was initialized */ + H5G_loc_t dset_loc; /* Dataset location */ + unsigned u; /* Local index variable */ + H5D_t *ret_value; /* Return value */ + + FUNC_ENTER_NOAPI(H5D_create, NULL) + + /* check args */ + HDassert(file); + HDassert(H5I_DATATYPE==H5I_get_type(type_id)); + HDassert(space); + HDassert(H5I_GENPROP_LST==H5I_get_type(dcpl_id)); + HDassert(H5I_GENPROP_LST==H5I_get_type(dxpl_id)); + + /* Get the dataset's datatype */ + if(NULL == (type = (const H5T_t *)H5I_object(type_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a datatype") + + /* Check if the datatype is "sensible" for use in a dataset */ + if(H5T_is_sensible(type) != TRUE) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "datatype is not sensible") + + /* Check if the datatype is/contains a VL-type */ + if(H5T_detect_class(type, H5T_VLEN)) + has_vl_type=TRUE; + + /* Check if the dataspace has an extent set (or is NULL) */ + if(!(H5S_has_extent(space)) ) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "dataspace extent has not been set.") + + /* Initialize the dataset object */ + if(NULL == (new_dset = H5FL_CALLOC(H5D_t))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + + /* Set up & reset dataset location */ + dset_loc.oloc = &(new_dset->oloc); + dset_loc.path = &(new_dset->path); + H5G_loc_reset(&dset_loc); + + /* Initialize the shared dataset space */ + if(NULL == (new_dset->shared = H5D_new(dcpl_id, TRUE, has_vl_type))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + + /* Copy & initialize datatype for dataset */ + if(H5D_init_type(file, new_dset, type_id, type) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy datatype") + + /* Copy & initialize dataspace for dataset */ + if(H5D_init_space(file, new_dset, space) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy dataspace") + + /* Set the dataset's checked_filters flag to enable writing */ + new_dset->shared->checked_filters = TRUE; + + /* Check if the dataset has a non-default DCPL & get important values, if so */ + if(new_dset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT) { + H5D_layout_t *layout; /* Dataset's layout information */ + H5O_pline_t *pline; /* Dataset's I/O pipeline information */ + H5O_fill_t *fill; /* Dataset's fill value info */ + + /* Check if the filters in the DCPL can be applied to this dataset */ + if(H5Z_can_apply(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_CANTINIT, NULL, "I/O filters can't operate on this dataset") + + /* Make the "set local" filter callbacks for this dataset */ + if(H5Z_set_local(new_dset->shared->dcpl_id, new_dset->shared->type_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set local filter parameters") + + /* Get new dataset's property list object */ + if(NULL == (dc_plist = (H5P_genplist_t *)H5I_object(new_dset->shared->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list") + + /* Retrieve the properties we need */ + pline = &new_dset->shared->dcpl_cache.pline; + if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, pline) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter") + layout = &new_dset->shared->layout.type; + if(H5P_get(dc_plist, H5D_CRT_LAYOUT_NAME, layout) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout") + if(pline->nused > 0 && H5D_CHUNKED != *layout) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout") + fill = &new_dset->shared->dcpl_cache.fill; + if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, fill) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill value info") + + /* Check if the alloc_time is the default and error out */ + if(fill->alloc_time == H5D_ALLOC_TIME_DEFAULT) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "invalid space allocation state") + + /* Don't allow compact datasets to allocate space later */ + if(*layout == H5D_COMPACT && fill->alloc_time != H5D_ALLOC_TIME_EARLY) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset must have early space allocation") + + /* If MPI VFD is used, no filter support yet. */ + if(IS_H5FD_MPI(file) && pline->nused > 0) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet") + + /* Chunked datasets are non-default, so retrieve their info here */ + if(H5P_get(dc_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk dimensions") + + /* Get the dataset's external file list information */ + if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &new_dset->shared->dcpl_cache.efl) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list") + } /* end if */ + + /* Set the latest version of the pline & fill messages, if requested */ + if(H5F_USE_LATEST_FORMAT(file)) { + /* Set the latest version for the I/O pipeline message */ + if(H5Z_set_latest_version(&new_dset->shared->dcpl_cache.pline) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of I/O filter pipeline") + + /* Set the latest version for the fill value message */ + if(H5O_fill_set_latest_version(&new_dset->shared->dcpl_cache.fill) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set latest version of fill value") + } /* end if */ + + /* Check if this dataset is going into a parallel file and set space allocation time */ + if(IS_H5FD_MPI(file)) + new_dset->shared->dcpl_cache.fill.alloc_time = H5D_ALLOC_TIME_EARLY; + + switch(new_dset->shared->layout.type) { + case H5D_CONTIGUOUS: + { + hssize_t tmp_size; /* Temporary holder for raw data size */ + hsize_t dim[H5O_LAYOUT_NDIMS]; /* Current size of data in elements */ + hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */ + + /* + * The maximum size of the dataset cannot exceed the storage size. + * Also, only the slowest varying dimension of a simple data space + * can be extendible (currently only for external data storage). + */ + new_dset->shared->layout.u.contig.addr = HADDR_UNDEF; /* Initialize to no address */ + + if((ndims = H5S_get_simple_extent_dims(new_dset->shared->space, dim, max_dim)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize contiguous storage") + for(i = 1; i < ndims; i++) + if(max_dim[i] > dim[i]) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible") + if(new_dset->shared->dcpl_cache.efl.nused > 0) { + hsize_t max_points = H5S_get_npoints_max(new_dset->shared->space); + hsize_t max_storage = H5O_efl_total_size(&new_dset->shared->dcpl_cache.efl); + + if(H5S_UNLIMITED == max_points) { + if(H5O_EFL_UNLIMITED != max_storage) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unlimited data space but finite storage") + } else if(max_points * H5T_get_size(type) < max_points) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space * type size overflowed") + } else if(max_points * H5T_get_size(type) > max_storage) { + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "data space size exceeds external storage size") + } + + /* Set the I/O functions for this layout type */ + new_dset->shared->io_ops.readvv = H5D_efl_readvv; + new_dset->shared->io_ops.writevv = H5D_efl_writevv; + } /* end if */ + else { + if(ndims > 0 && max_dim[0] > dim[0]) + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset") + + /* Set the I/O functions for this layout type */ + new_dset->shared->io_ops.readvv = H5D_contig_readvv; + new_dset->shared->io_ops.writevv = H5D_contig_writevv; + } /* end else */ + + /* Compute the total size of a chunk */ + tmp_size = H5S_GET_EXTENT_NPOINTS(new_dset->shared->space) * H5T_get_size(new_dset->shared->type); + H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t); + + /* Get the sieve buffer size for this dataset */ + new_dset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(file); + } /* end case */ + break; + + case H5D_CHUNKED: + { + hsize_t max_dim[H5O_LAYOUT_NDIMS]; /* Maximum size of data in elements */ + + /* Set up layout information */ + if((ndims = H5S_GET_EXTENT_NDIMS(new_dset->shared->space)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "unable to get rank") + new_dset->shared->layout.u.chunk.ndims = (unsigned)ndims + 1; + HDassert((unsigned)(new_dset->shared->layout.u.chunk.ndims) <= NELMTS(new_dset->shared->layout.u.chunk.dim)); + + /* Initialize to no address */ + new_dset->shared->layout.u.chunk.addr = HADDR_UNDEF; + + /* + * Chunked storage allows any type of data space extension, so we + * don't even bother checking. + */ + if(chunk_ndims != (unsigned)ndims) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space") + if(new_dset->shared->dcpl_cache.efl.nused > 0) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout") + + /* + * The chunk size of a dimension with a fixed size cannot exceed + * the maximum dimension size + */ + if(H5P_get(dc_plist, H5D_CRT_CHUNK_SIZE_NAME, new_dset->shared->layout.u.chunk.dim) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size") + new_dset->shared->layout.u.chunk.dim[new_dset->shared->layout.u.chunk.ndims-1] = H5T_get_size(new_dset->shared->type); + + if(H5S_get_simple_extent_dims(new_dset->shared->space, NULL, max_dim) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions") + for(u = 0; u < new_dset->shared->layout.u.chunk.ndims - 1; u++) + if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < new_dset->shared->layout.u.chunk.dim[u]) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions") + + /* Compute the total size of a chunk */ + for(u = 1, new_dset->shared->layout.u.chunk.size = new_dset->shared->layout.u.chunk.dim[0]; u < new_dset->shared->layout.u.chunk.ndims; u++) + new_dset->shared->layout.u.chunk.size *= new_dset->shared->layout.u.chunk.dim[u]; + + /* Set the I/O functions for this layout type */ + new_dset->shared->io_ops.readvv = H5D_istore_readvv; + new_dset->shared->io_ops.writevv = H5D_istore_writevv; + + /* Initialize the chunk cache for the dataset */ + if(H5D_istore_init(file, new_dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't initialize chunk cache") + + /* Indicate that the chunk information was initialized */ + chunk_init = TRUE; + } /* end case */ + break; + + case H5D_COMPACT: + { + hssize_t tmp_size; /* Temporary holder for raw data size */ + hsize_t comp_data_size; + + /* + * Compact dataset is stored in dataset object header message of + * layout. + */ + tmp_size = H5S_GET_EXTENT_NPOINTS(space) * H5T_get_size(new_dset->shared->type); + H5_ASSIGN_OVERFLOW(new_dset->shared->layout.u.compact.size, tmp_size, hssize_t, size_t); + + /* Verify data size is smaller than maximum header message size + * (64KB) minus other layout message fields. + */ + comp_data_size = H5O_MESG_MAX_SIZE - H5O_layout_meta_size(file, &(new_dset->shared->layout)); + if(new_dset->shared->layout.u.compact.size > comp_data_size) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size") + + /* Set the I/O functions for this layout type */ + new_dset->shared->io_ops.readvv = H5D_compact_readvv; + new_dset->shared->io_ops.writevv = H5D_compact_writevv; + } /* end case */ + break; + + default: + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet") + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + + /* Update the dataset's object header info. */ + if(H5D_update_oh_info(file, dxpl_id, new_dset) != SUCCEED) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't update the metadata cache") + + /* Add the dataset to the list of opened objects in the file */ + if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count") + if(H5FO_insert(new_dset->oloc.file, new_dset->oloc.addr, new_dset->shared, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects") + + new_dset->shared->fo_count = 1; + + /* Success */ + ret_value = new_dset; + +done: + if(!ret_value && new_dset && new_dset->shared) { + if(new_dset->shared) { + if(new_dset->shared->layout.type == H5D_CHUNKED && chunk_init) { + if(H5D_istore_dest(new_dset,H5AC_dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, NULL, "unable to destroy chunk cache") + } /* end if */ + if(new_dset->shared->space) { + if(H5S_close(new_dset->shared->space) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release dataspace") + } /* end if */ + if(new_dset->shared->type) { + if(H5I_dec_ref(new_dset->shared->type_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release datatype") + } /* end if */ + if(H5F_addr_defined(new_dset->oloc.addr)) { + if(H5O_close(&(new_dset->oloc)) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, NULL, "unable to release object header") + if(file) { + if(H5O_delete(file, dxpl_id, new_dset->oloc.addr) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDELETE, NULL, "unable to delete object header") + } /* end if */ + } /* end if */ + if(new_dset->shared->dcpl_id != 0) { + if(H5I_dec_ref(new_dset->shared->dcpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list") + } /* end if */ + H5FL_FREE(H5D_shared_t, new_dset->shared); + } /* end if */ + new_dset->oloc.file = NULL; + H5FL_FREE(H5D_t, new_dset); + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_create() */ + + +/* + *------------------------------------------------------------------------- + * Function: H5D_open + * + * Purpose: Checks if dataset is already open, or opens a dataset for + * access. + * + * Return: Success: Dataset ID + * Failure: FAIL + * + * Programmer: Quincey Koziol + * Friday, December 20, 2002 + * + *------------------------------------------------------------------------- + */ +H5D_t * +H5D_open(const H5G_loc_t *loc, hid_t dxpl_id) +{ + H5D_shared_t *shared_fo = NULL; + H5D_t *dataset = NULL; + H5D_t *ret_value; /* Return value */ + + FUNC_ENTER_NOAPI(H5D_open, NULL) + + /* check args */ + HDassert(loc); + + /* Allocate the dataset structure */ + if(NULL == (dataset = H5FL_CALLOC(H5D_t))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + + /* Shallow copy (take ownership) of the object location object */ + if(H5O_loc_copy(&(dataset->oloc), loc->oloc, H5_COPY_SHALLOW) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy object location") + + /* Shallow copy (take ownership) of the group hier. path */ + if(H5G_name_copy(&(dataset->path), loc->path, H5_COPY_SHALLOW) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy path") + + /* Check if dataset was already open */ + if((shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr)) == NULL) { + /* Clear any errors from H5FO_opened() */ + H5E_clear_stack(NULL); + + /* Open the dataset object */ + if(H5D_open_oid(dataset, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found") + + /* Add the dataset to the list of opened objects in the file */ + if(H5FO_insert(dataset->oloc.file, dataset->oloc.addr, dataset->shared, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, NULL, "can't insert dataset into list of open objects") + + /* Increment object count for the object in the top file */ + if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count") + + /* We're the first dataset to use the the shared info */ + dataset->shared->fo_count = 1; + } /* end if */ + else { + /* Point to shared info */ + dataset->shared = shared_fo; + + /* Increment # of datasets using shared information */ + shared_fo->fo_count++; + + /* Check if the object has been opened through the top file yet */ + if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) { + /* Open the object through this top file */ + if(H5O_open(&(dataset->oloc)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open object header") + } /* end if */ + + /* Increment object count for the object in the top file */ + if(H5FO_top_incr(dataset->oloc.file, dataset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't increment object count") + } /* end else */ + + ret_value = dataset; + +done: + if(ret_value == NULL) { + /* Free the location--casting away const*/ + if(dataset) { + if(shared_fo == NULL) /* Need to free shared fo */ + H5FL_FREE(H5D_shared_t, dataset->shared); + + H5O_loc_free(&(dataset->oloc)); + H5G_name_free(&(dataset->path)); + + H5FL_FREE(H5D_t, dataset); + } + if(shared_fo) + shared_fo->fo_count--; + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_open() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_open_oid + * + * Purpose: Opens a dataset for access. + * + * Return: Dataset pointer on success, NULL on failure + * + * Programmer: Quincey Koziol + * Monday, October 12, 1998 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_open_oid(H5D_t *dataset, hid_t dxpl_id) +{ + H5P_genplist_t *plist; /* Property list */ + H5O_pline_t *pline; /* I/O pipeline information */ + H5O_fill_t *fill_prop; /* Pointer to dataset's fill value info */ + unsigned alloc_time_state; /* Allocation time state */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_open_oid) + + /* check args */ + HDassert(dataset); + + /* (Set the 'vl_type' parameter to FALSE since it doesn't matter from here) */ + if(NULL == (dataset->shared = H5D_new(H5P_DATASET_CREATE_DEFAULT, FALSE, FALSE))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") + + /* Open the dataset object */ + if(H5O_open(&(dataset->oloc)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open") + + /* Get the type and space */ + if(NULL == (dataset->shared->type = (H5T_t *)H5O_msg_read(&(dataset->oloc), H5O_DTYPE_ID, NULL, dxpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load type info from dataset header") + if(NULL == (dataset->shared->space = H5S_read(&(dataset->oloc), dxpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to load space info from dataset header") + + /* Get a datatype ID for the dataset's datatype */ + if((dataset->shared->type_id = H5I_register(H5I_DATATYPE, dataset->shared->type)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register type") + + /* Get dataset creation property list object */ + if(NULL == (plist = (H5P_genplist_t *)H5I_object(dataset->shared->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get dataset creation property list") + + /* Get the optional filters message */ + pline = &dataset->shared->dcpl_cache.pline; + if(NULL != H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, pline, dxpl_id)) { + if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, pline) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set pipeline") + } /* end if */ + else + H5E_clear_stack(NULL); + + /* + * Get the raw data layout info. It's actually stored in two locations: + * the storage message of the dataset (dataset->storage) and certain + * values are copied to the dataset create plist so the user can query + * them. + */ + if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message") + if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->shared->layout.type) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout") + switch(dataset->shared->layout.type) { + case H5D_CONTIGUOUS: + /* Compute the size of the contiguous storage for versions of the + * layout message less than version 3 because versions 1 & 2 would + * truncate the dimension sizes to 32-bits of information. - QAK 5/26/04 + */ + if(dataset->shared->layout.version < 3) { + hssize_t tmp_size; /* Temporary holder for raw data size */ + + tmp_size = H5S_GET_EXTENT_NPOINTS(dataset->shared->space) * H5T_get_size(dataset->shared->type); + H5_ASSIGN_OVERFLOW(dataset->shared->layout.u.contig.size, tmp_size, hssize_t, hsize_t); + } /* end if */ + + /* Set the I/O functions for this layout type */ + dataset->shared->io_ops.readvv = H5D_contig_readvv; + dataset->shared->io_ops.writevv = H5D_contig_writevv; + + /* Get the sieve buffer size for this dataset */ + dataset->shared->cache.contig.sieve_buf_size = H5F_SIEVE_BUF_SIZE(dataset->oloc.file); + break; + + case H5D_CHUNKED: + /* + * Chunked storage. The creation plist's dimension is one less than + * the chunk dimension because the chunk includes a dimension for the + * individual bytes of the datatype. + */ + { + unsigned chunk_ndims; /* Dimensionality of chunk */ + + chunk_ndims = dataset->shared->layout.u.chunk.ndims - 1; + + if(H5P_set(plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk dimensions") + if(H5P_set(plist, H5D_CRT_CHUNK_SIZE_NAME, dataset->shared->layout.u.chunk.dim) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set chunk size") + + /* Initialize the chunk cache for the dataset */ + if(H5D_istore_init(dataset->oloc.file, dataset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache") + } + + /* Set the I/O functions for this layout type */ + dataset->shared->io_ops.readvv = H5D_istore_readvv; + dataset->shared->io_ops.writevv = H5D_istore_writevv; + break; + + case H5D_COMPACT: + /* Set the I/O functions for this layout type */ + dataset->shared->io_ops.readvv = H5D_compact_readvv; + dataset->shared->io_ops.writevv = H5D_compact_writevv; + break; + + default: + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet") + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + + /* Point at dataset's copy, to cache it for later */ + fill_prop = &dataset->shared->dcpl_cache.fill; + + /* Try to get the new fill value message from the object header */ + if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_NEW_ID, fill_prop, dxpl_id)) { + H5E_clear_stack(NULL); + + /* For backward compatibility, try to retrieve the old fill value message */ + if(NULL == H5O_msg_read(&(dataset->oloc), H5O_FILL_ID, fill_prop, dxpl_id)) { + H5E_clear_stack(NULL); + + /* Set the space allocation time appropriately, based on the type of dataset storage */ + switch(dataset->shared->layout.type) { + case H5D_COMPACT: + fill_prop->alloc_time = H5D_ALLOC_TIME_EARLY; + break; + + case H5D_CONTIGUOUS: + fill_prop->alloc_time = H5D_ALLOC_TIME_LATE; + break; + + case H5D_CHUNKED: + fill_prop->alloc_time = H5D_ALLOC_TIME_INCR; + break; + + default: + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet") + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + } /* end if */ + + /* If "old" fill value size is 0 (undefined), map it to -1 */ + if(fill_prop->size == 0) + fill_prop->size = (size_t)-1; + } /* end if */ + alloc_time_state = 0; + if((dataset->shared->layout.type == H5D_COMPACT && fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) + || (dataset->shared->layout.type == H5D_CONTIGUOUS && fill_prop->alloc_time == H5D_ALLOC_TIME_LATE) + || (dataset->shared->layout.type == H5D_CHUNKED && fill_prop->alloc_time == H5D_ALLOC_TIME_INCR)) + alloc_time_state = 1; + + /* Set revised fill value properties, if they are different from the defaults */ + if(H5P_fill_value_cmp(&H5D_def_dset.dcpl_cache.fill, fill_prop, sizeof(H5O_fill_t))) { + if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, fill_prop) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set fill value") + if(H5P_set(plist, H5D_CRT_ALLOC_TIME_STATE_NAME, &alloc_time_state) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set allocation time state") + } /* end if */ + + /* Get the external file list message, which might not exist. Space is + * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */ + if((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr)) + || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) { + if(NULL != H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id)) { + if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list") + + /* Override the I/O functions for this layout type */ + dataset->shared->io_ops.readvv = H5D_efl_readvv; + dataset->shared->io_ops.writevv = H5D_efl_writevv; + } /* end if */ + else + H5E_clear_stack(NULL); + } /* end if */ + + /* + * Make sure all storage is properly initialized. + * This is important only for parallel I/O where the space must + * be fully allocated before I/O can happen. + */ + if((H5F_get_intent(dataset->oloc.file) & H5F_ACC_RDWR) + && ((dataset->shared->layout.type == H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr)) + || (dataset->shared->layout.type == H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) + && IS_H5FD_MPI(dataset->oloc.file)) { + if(H5D_alloc_storage(dataset->oloc.file, dxpl_id, dataset, H5D_ALLOC_OPEN, TRUE, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file storage") + } /* end if */ + +done: + if(ret_value < 0) { + if(H5F_addr_defined(dataset->oloc.addr)) { + if(H5O_close(&(dataset->oloc)) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") + } /* end if */ + if(dataset->shared->space) { + if(H5S_close(dataset->shared->space) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") + } /* end if */ + if(dataset->shared->type) { + if(dataset->shared->type_id > 0) { + if(H5I_dec_ref(dataset->shared->type_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") + } /* end if */ + else { + if(H5T_close(dataset->shared->type) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release datatype") + } /* end else */ + } /* end if */ + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_open_oid() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_close + * + * Purpose: Insures that all data has been saved to the file, closes the + * dataset object header, and frees all resources used by the + * descriptor. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Robb Matzke + * Thursday, December 4, 1997 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_close(H5D_t *dataset) +{ + unsigned free_failed = FALSE; + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5D_close, FAIL) + + /* check args */ + HDassert(dataset && dataset->oloc.file && dataset->shared); + HDassert(dataset->shared->fo_count >0); + + /* Dump debugging info */ +#ifdef H5D_ISTORE_DEBUG + H5D_istore_stats(dataset, FALSE); +#endif /* H5F_ISTORE_DEBUG */ + + dataset->shared->fo_count--; + if(dataset->shared->fo_count == 0) { + /* Free the data sieve buffer, if it's been allocated */ + if(dataset->shared->cache.contig.sieve_buf) { + HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ + + /* Flush the raw data buffer, if its dirty */ + if(dataset->shared->cache.contig.sieve_dirty) { + /* Write dirty data sieve buffer to file */ + if(H5F_block_write(dataset->oloc.file, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, + dataset->shared->cache.contig.sieve_size, H5AC_dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") + + /* Reset sieve buffer dirty flag */ + dataset->shared->cache.contig.sieve_dirty = FALSE; + } /* end if */ + + dataset->shared->cache.contig.sieve_buf = (unsigned char *)H5FL_BLK_FREE(sieve_buf,dataset->shared->cache.contig.sieve_buf); + } /* end if */ + + /* Free cached information for each kind of dataset */ + switch(dataset->shared->layout.type) { + case H5D_CONTIGUOUS: + break; + + case H5D_CHUNKED: + /* Flush and destroy chunks in the cache */ + if(H5D_istore_dest(dataset,H5AC_dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache") + break; + + case H5D_COMPACT: + /* Update header message of layout for compact dataset. */ + if(dataset->shared->layout.u.compact.dirty) { + if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), H5AC_dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to update layout message") + dataset->shared->layout.u.compact.dirty = FALSE; + } /* end if */ + + /* Free the buffer for the raw data for compact datasets */ + dataset->shared->layout.u.compact.buf = H5MM_xfree(dataset->shared->layout.u.compact.buf); + break; + + default: + HDassert("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") +#endif /* NDEBUG */ + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + + /* + * Release datatype, dataspace and creation property list -- there isn't + * much we can do if one of these fails, so we just continue. + */ + free_failed = (H5I_dec_ref(dataset->shared->type_id) < 0 || H5S_close(dataset->shared->space) < 0 || + H5I_dec_ref(dataset->shared->dcpl_id) < 0); + + /* Remove the dataset from the list of opened objects in the file */ + if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") + if(H5FO_delete(dataset->oloc.file, H5AC_dxpl_id, dataset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't remove dataset from list of open objects") + + /* Close the dataset object */ + /* (This closes the file, if this is the last object open) */ + if(H5O_close(&(dataset->oloc)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release object header") + + /* + * Free memory. Before freeing the memory set the file pointer to NULL. + * We always check for a null file pointer in other H5D functions to be + * sure we're not accessing an already freed dataset (see the HDassert() + * above). + */ + dataset->oloc.file = NULL; + + H5FL_FREE(H5D_shared_t, dataset->shared); + } /* end if */ + else { + /* Decrement the ref. count for this object in the top file */ + if(H5FO_top_decr(dataset->oloc.file, dataset->oloc.addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't decrement count for object") + + /* Check reference count for this object in the top file */ + if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) + if(H5O_close(&(dataset->oloc)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to close") + } /* end else */ + + /* Release the dataset's path info */ + if(H5G_name_free(&(dataset->path)) < 0) + free_failed = TRUE; + + /* Free the dataset's memory structure */ + H5FL_FREE(H5D_t, dataset); + + /* Check if anything failed in the middle... */ + if(free_failed) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free a component of the dataset, but the dataset was freed anyway.") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_close() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_oloc + * + * Purpose: Returns a pointer to the object location for a dataset. + * + * Return: Success: Ptr to location + * Failure: NULL + * + * Programmer: Robb Matzke + * Friday, April 24, 1998 + * + *------------------------------------------------------------------------- + */ +H5O_loc_t * +H5D_oloc(H5D_t *dataset) +{ + /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_oloc) + + FUNC_LEAVE_NOAPI(dataset ? &(dataset->oloc) : (H5O_loc_t *)NULL) +} /* end H5D_oloc() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_nameof + * + * Purpose: Returns a pointer to the group hier. path for a dataset. + * + * Return: Success: Ptr to entry + * Failure: NULL + * + * Programmer: Quincey Koziol + * Monday, September 12, 2005 + * + *------------------------------------------------------------------------- + */ +H5G_name_t * +H5D_nameof(H5D_t *dataset) +{ + /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_nameof) + + FUNC_LEAVE_NOAPI(dataset ? &(dataset->path) : (H5G_name_t *)NULL) +} /* end H5D_nameof() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_typeof + * + * Purpose: Returns a pointer to the dataset's datatype. The datatype + * is not copied. + * + * Return: Success: Ptr to the dataset's datatype, uncopied. + * + * Failure: NULL + * + * Programmer: Robb Matzke + * Thursday, June 4, 1998 + * + *------------------------------------------------------------------------- + */ +H5T_t * +H5D_typeof(const H5D_t *dset) +{ + /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_typeof) + + HDassert(dset); + HDassert(dset->shared->type); + + FUNC_LEAVE_NOAPI(dset->shared->type) +} /* end H5D_typeof() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_get_file + * + * Purpose: Returns the dataset's file pointer. + * + * Return: Success: Ptr to the dataset's file pointer. + * + * Failure: NULL + * + * Programmer: Quincey Koziol + * Thursday, October 22, 1998 + * + *------------------------------------------------------------------------- + */ +static H5F_t * +H5D_get_file(const H5D_t *dset) +{ + /* Use FUNC_ENTER_NOAPI_NOINIT_NOFUNC here to avoid performance issues */ + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_get_file) + + HDassert(dset); + HDassert(dset->oloc.file); + + FUNC_LEAVE_NOAPI(dset->oloc.file) +} /* end H5D_get_file() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_alloc_storage + * + * Purpose: Allocate storage for the raw data of a dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Robb Matzke + * Friday, January 16, 1998 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc, + hbool_t update_time, hbool_t full_overwrite) +{ + struct H5O_layout_t *layout; /* The dataset's layout information */ + hbool_t must_init_space = FALSE; /* Flag to indicate that space should be initialized */ + hbool_t addr_set = FALSE; /* Flag to indicate that the dataset's storage address was set */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_alloc_storage) + + /* check args */ + HDassert(f); + HDassert(dset); + + /* If the data is stored in external files, don't set an address for the layout + * We assume that external storage is already + * allocated by the caller, or at least will be before I/O is performed. + */ + if(!(H5S_NULL == H5S_GET_EXTENT_TYPE(dset->shared->space) || dset->shared->dcpl_cache.efl.nused > 0)) { + /* Get a pointer to the dataset's layout information */ + layout = &(dset->shared->layout); + + switch(layout->type) { + case H5D_CONTIGUOUS: + if(!H5F_addr_defined(layout->u.contig.addr)) { + /* Reserve space in the file for the entire array */ + if(H5D_contig_create(f, dxpl_id, layout/*out*/) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage") + + /* Indicate that we set the storage addr */ + addr_set = TRUE; + + /* Indicate that we should initialize storage space */ + must_init_space = TRUE; + } /* end if */ + break; + + case H5D_CHUNKED: + if(!H5F_addr_defined(layout->u.chunk.addr)) { + /* Create the root of the B-tree that describes chunked storage */ + if(H5D_istore_create(f, dxpl_id, layout/*out*/) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage") + + /* Indicate that we set the storage addr */ + addr_set = TRUE; + + /* Indicate that we should initialize storage space */ + must_init_space = TRUE; + } /* end if */ + + /* If space allocation is set to 'early' and we are extending + * the dataset, indicate that space should be allocated, so the + * B-tree gets expanded. -QAK + */ + if(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY + && time_alloc == H5D_ALLOC_EXTEND) + must_init_space = 1; + break; + + case H5D_COMPACT: + /* Check if space is already allocated */ + if(layout->u.compact.buf==NULL) { + /* Reserve space in layout header message for the entire array. */ + HDassert(layout->u.compact.size > 0); + if(NULL == (layout->u.compact.buf = H5MM_malloc(layout->u.compact.size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset") + if(!full_overwrite) + HDmemset(layout->u.compact.buf, 0, layout->u.compact.size); + layout->u.compact.dirty = TRUE; + + /* Indicate that we set the storage addr */ + addr_set = TRUE; + + /* Indicate that we should initialize storage space */ + must_init_space = TRUE; + } /* end if */ + break; + + default: + HDassert("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") +#endif /* NDEBUG */ + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + + /* Check if we need to initialize the space */ + if(must_init_space) { + if(layout->type == H5D_CHUNKED) { + /* If we are doing incremental allocation and the B-tree got + * created during a H5Dwrite call, don't initialize the storage + * now, wait for the actual writes to each block and let the + * low-level chunking routines handle initialize the fill-values. + * Otherwise, pass along the space initialization call and let + * the low-level chunking routines sort out whether to write + * fill values to the chunks they allocate space for. Yes, + * this is icky. -QAK + */ + if(!(dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_INCR && time_alloc == H5D_ALLOC_WRITE)) + if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") + } /* end if */ + else { + H5D_fill_value_t fill_status; /* The fill value status */ + + /* Check the dataset's fill-value status */ + if(H5P_is_fill_value_defined(&dset->shared->dcpl_cache.fill, &fill_status) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") + + /* If we are filling the dataset on allocation or "if set" and + * the fill value _is_ set, do that now */ + if(dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || + (dset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) { + if(H5D_init_storage(dset, full_overwrite, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value") + } /* end if */ + } /* end else */ + } /* end if */ + + /* Also update header message for layout with new address, if we + * set the address. (this is improves forward compatibility). + */ + if(time_alloc != H5D_ALLOC_CREATE && addr_set) + if(H5O_msg_write(&dset->oloc, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_time, &dset->shared->layout, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message") + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_alloc_storage() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_init_storage + * + * Purpose: Initialize the data for a new dataset. If a selection is + * defined for SPACE then initialize only that part of the + * dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Robb Matzke + * Monday, October 5, 1998 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_init_storage) + + HDassert(dset); + + switch (dset->shared->layout.type) { + case H5D_COMPACT: + /* If we will be immediately overwriting the values, don't bother to clear them */ + if(!full_overwrite) { + /* Fill the compact dataset storage */ + if(H5D_compact_fill(dset, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize compact dataset storage") + } /* end if */ + break; + + case H5D_CONTIGUOUS: + /* Don't write default fill values to external files */ + /* If we will be immediately overwriting the values, don't bother to clear them */ + if((dset->shared->dcpl_cache.efl.nused == 0 || dset->shared->dcpl_cache.fill.buf) && !full_overwrite) + if(H5D_contig_fill(dset, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") + break; + + case H5D_CHUNKED: + /* + * Allocate file space + * for all chunks now and initialize each chunk with the fill value. + */ + if(H5D_istore_allocate(dset, dxpl_id, full_overwrite) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset") + break; + + default: + HDassert("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") +#endif /* NDEBUG */ + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_init_storage() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_get_storage_size + * + * Purpose: Determines how much space has been reserved to store the raw + * data of a dataset. + * + * Return: Success: Number of bytes reserved to hold raw data. + * + * Failure: 0 + * + * Programmer: Robb Matzke + * Wednesday, April 21, 1999 + * + *------------------------------------------------------------------------- + */ +hsize_t +H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id) +{ + hsize_t ret_value; + + FUNC_ENTER_NOAPI_NOINIT(H5D_get_storage_size) + + switch(dset->shared->layout.type) { + case H5D_CHUNKED: + if(dset->shared->layout.u.chunk.addr == HADDR_UNDEF) + ret_value = 0; + else + ret_value = H5D_istore_allocated(dset, dxpl_id); + break; + + case H5D_CONTIGUOUS: + /* Datasets which are not allocated yet are using no space on disk */ + if(dset->shared->layout.u.contig.addr == HADDR_UNDEF) + ret_value = 0; + else + ret_value = dset->shared->layout.u.contig.size; + break; + + case H5D_COMPACT: + ret_value = dset->shared->layout.u.compact.size; + break; + + default: + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset type") + } /*lint !e788 All appropriate cases are covered */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_get_storage_size() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_get_offset + * + * Purpose: Private function for H5D_get_offset. Returns the address + * of dataset in file. + * + * Return: Success: the address of dataset + * + * Failure: HADDR_UNDEF + * + * Programmer: Raymond Lu + * November 6, 2002 + * + *------------------------------------------------------------------------- + */ +haddr_t +H5D_get_offset(const H5D_t *dset) +{ + haddr_t base_addr; + H5F_t *f; + haddr_t ret_value = HADDR_UNDEF; + + FUNC_ENTER_NOAPI_NOINIT(H5D_get_offset) + + HDassert(dset); + + switch(dset->shared->layout.type) { + case H5D_CHUNKED: + case H5D_COMPACT: + break; + + case H5D_CONTIGUOUS: + /* If dataspace hasn't been allocated or dataset is stored in + * an external file, the value will be HADDR_UNDEF. */ + f = H5D_get_file(dset); + base_addr = H5F_get_base_addr(f); + + /* If there's user block in file, returns the absolute dataset offset + * from the beginning of file. */ + if(base_addr != HADDR_UNDEF) + ret_value = dset->shared->layout.u.contig.addr + base_addr; + else + ret_value = dset->shared->layout.u.contig.addr; + break; + + default: + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, HADDR_UNDEF, "unknown dataset layout type") + } /*lint !e788 All appropriate cases are covered */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_get_offset() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_iterate + * + * Purpose: Internal version of H5Diterate() + * + * Return: Returns the return value of the last operator if it was non-zero, + * or zero if all elements were processed. Otherwise returns a + * negative value. + * + * Programmer: Quincey Koziol + * Tuesday, November 22, 2005 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t op, + void *operator_data) +{ + herr_t ret_value; + + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_iterate) + + /* Check args */ + HDassert(buf); + HDassert(H5I_DATATYPE == H5I_get_type(type_id)); + HDassert(space); + HDassert(H5S_has_extent(space)); + HDassert(op); + + ret_value = H5S_select_iterate(buf, type_id, space, op, operator_data); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_iterate() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_vlen_reclaim + * + * Purpose: Frees the buffers allocated for storing variable-length data + * in memory. Only frees the VL data in the selection defined in the + * dataspace. The dataset transfer property list is required to find the + * correct allocation/free methods for the VL data in the buffer. + * + * Return: Non-negative on success, negative on failure + * + * Programmer: Quincey Koziol + * Tuesday, November 22, 2005 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_vlen_reclaim(hid_t type_id, H5S_t *space, hid_t plist_id, void *buf) +{ + H5T_vlen_alloc_info_t _vl_alloc_info; /* VL allocation info buffer */ + H5T_vlen_alloc_info_t *vl_alloc_info = &_vl_alloc_info; /* VL allocation info */ + herr_t ret_value; + + FUNC_ENTER_NOAPI(H5D_vlen_reclaim, FAIL) + + /* Check args */ + HDassert(H5I_DATATYPE == H5I_get_type(type_id)); + HDassert(space); + HDassert(H5P_isa_class(plist_id, H5P_DATASET_XFER)); + HDassert(buf); + + /* Get the allocation info */ + if(H5T_vlen_get_alloc_info(plist_id,&vl_alloc_info) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "unable to retrieve VL allocation info") + + /* Call H5D_iterate with args, etc. */ + ret_value = H5D_iterate(buf, type_id, space ,H5T_vlen_reclaim, vl_alloc_info); + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_vlen_reclaim() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_vlen_get_buf_size_alloc + * + * Purpose: This routine makes certain there is enough space in the temporary + * buffer for the new data to read in. All the VL data read in is actually + * placed in this buffer, overwriting the previous data. Needless to say, + * this data is not actually usable. + * + * Return: Non-negative on success, negative on failure + * + * Programmer: Quincey Koziol + * Tuesday, August 17, 1999 + * + *------------------------------------------------------------------------- + */ +void * +H5D_vlen_get_buf_size_alloc(size_t size, void *info) +{ + H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)info; + void *ret_value; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_vlen_get_buf_size_alloc) + + /* Get a temporary pointer to space for the VL data */ + if((vlen_bufsize->vl_tbuf = H5FL_BLK_REALLOC(vlen_vl_buf, vlen_bufsize->vl_tbuf, size)) != NULL) + vlen_bufsize->size += size; + + /* Set return value */ + ret_value = vlen_bufsize->vl_tbuf; + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_vlen_get_buf_size_alloc() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_vlen_get_buf_size + * + * Purpose: This routine checks the number of bytes required to store a single + * element from a dataset in memory, creating a selection with just the + * single element selected to read in the element and using a custom memory + * allocator for any VL data encountered. + * The *size value is modified according to how many bytes are + * required to store the element in memory. + * + * Implementation: This routine actually performs the read with a custom + * memory manager which basically just counts the bytes requested and + * uses a temporary memory buffer (through the H5FL API) to make certain + * enough space is available to perform the read. Then the temporary + * buffer is released and the number of bytes allocated is returned. + * Kinda kludgy, but easier than the other method of trying to figure out + * the sizes without actually reading the data in... - QAK + * + * Return: Non-negative on success, negative on failure + * + * Programmer: Quincey Koziol + * Tuesday, August 17, 1999 + * + *------------------------------------------------------------------------- + */ +/* ARGSUSED */ +herr_t +H5D_vlen_get_buf_size(void UNUSED *elem, hid_t type_id, unsigned UNUSED ndim, const hsize_t *point, void *op_data) +{ + H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)op_data; + H5T_t *dt; /* Datatype for operation */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_vlen_get_buf_size) + + HDassert(op_data); + HDassert(H5I_DATATYPE == H5I_get_type(type_id)); + + /* Check args */ + if(NULL == (dt = (H5T_t *)H5I_object(type_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype") + + /* Make certain there is enough fixed-length buffer available */ + if(NULL == (vlen_bufsize->fl_tbuf = H5FL_BLK_REALLOC(vlen_fl_buf, vlen_bufsize->fl_tbuf, H5T_get_size(dt)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't resize tbuf") + + /* Select point to read in */ + if(H5Sselect_elements(vlen_bufsize->fspace_id, H5S_SELECT_SET, (size_t)1, (const hsize_t **)point) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't select point") + + /* Read in the point (with the custom VL memory allocator) */ + if(H5Dread(vlen_bufsize->dataset_id, type_id, vlen_bufsize->mspace_id, vlen_bufsize->fspace_id, vlen_bufsize->xfer_pid, vlen_bufsize->fl_tbuf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_vlen_get_buf_size() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_check_filters + * + * Purpose: Check if the filters have be initialized for the dataset + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, October 11, 2007 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_check_filters(H5D_t *dataset) +{ + H5O_fill_t *fill; /* Dataset's fill value */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_check_filters) + + /* Check args */ + HDassert(dataset); + + /* Check if the filters in the DCPL will need to encode, and if so, can they? + * + * Filters need encoding if fill value is defined and a fill policy is set + * that requires writing on an extend. + */ + fill = &dataset->shared->dcpl_cache.fill; + if(!dataset->shared->checked_filters) { + H5D_fill_value_t fill_status; /* Whether the fill value is defined */ + + /* Retrieve the "defined" status of the fill value */ + if(H5P_is_fill_value_defined(fill, &fill_status) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Couldn't retrieve fill value from dataset.") + + /* See if we can check the filter status */ + if(fill_status == H5D_FILL_VALUE_DEFAULT || fill_status == H5D_FILL_VALUE_USER_DEFINED) { + if(fill->fill_time == H5D_FILL_TIME_ALLOC || + (fill->fill_time == H5D_FILL_TIME_IFSET && fill_status == H5D_FILL_VALUE_USER_DEFINED)) { + /* Filters must have encoding enabled. Ensure that all filters can be applied */ + if(H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0) + HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters") + + dataset->shared->checked_filters = TRUE; + } /* end if */ + } /* end if */ + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_check_filters() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_set_extent + * + * Purpose: Based on H5D_extend, allows change to a lower dimension, + * calls H5S_set_extent and H5D_istore_prune_by_extent instead + * + * Return: Non-negative on success, negative on failure + * + * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu + * April 9, 2002 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id) +{ + H5S_t *space; /* Dataset's dataspace */ + int rank; /* Dataspace # of dimensions */ + hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dimension sizes */ + htri_t changed; /* Whether the dataspace changed size */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_set_extent) + + /* Check args */ + HDassert(dset); + HDassert(size); + + /* Check if the filters in the DCPL will need to encode, and if so, can they? */ + if(H5D_check_filters(dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't apply filters") + + /* Get the data space */ + space = dset->shared->space; + + /* Check if we are shrinking or expanding any of the dimensions */ + if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") + + /* Modify the size of the data space */ + if((changed = H5S_set_extent(space, size)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + + /* Don't bother updating things, unless they've changed */ + if(changed) { + hbool_t shrink = FALSE; /* Flag to indicate a dimension has shrank */ + hbool_t expand = FALSE; /* Flag to indicate a dimension has grown */ + unsigned u; /* Local index variable */ + + /* Determine if we are shrinking and/or expanding any dimensions */ + for(u = 0; u < (unsigned)rank; u++) { + if(size[u] < curr_dims[u]) + shrink = TRUE; + if(size[u] > curr_dims[u]) + expand = TRUE; + } /* end for */ + + /*------------------------------------------------------------------------- + * Modify the dataset storage + *------------------------------------------------------------------------- + */ + /* Save the new dataspace in the file if necessary */ + if(H5S_write(&(dset->oloc), space, TRUE, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace") + + /* Update the index values for the cached chunks for this dataset */ + if(H5D_CHUNKED == dset->shared->layout.type) + if(H5D_istore_update_cache(dset, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices") + + /* Allocate space for the new parts of the dataset, if appropriate */ + if(expand && dset->shared->dcpl_cache.fill.alloc_time == H5D_ALLOC_TIME_EARLY) + if(H5D_alloc_storage(dset->oloc.file, dxpl_id, dset, H5D_ALLOC_EXTEND, TRUE, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset storage") + + + /*------------------------------------------------------------------------- + * Remove chunk information in the case of chunked datasets + * This removal takes place only in case we are shrinking the dateset + *------------------------------------------------------------------------- + */ + if(shrink && H5D_CHUNKED == dset->shared->layout.type) { + H5D_io_info_t io_info; /* Dataset I/O info */ + H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ + H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ + + /* Fill the DXPL cache values for later use */ + if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") + + /* Construct dataset I/O info */ + H5D_BUILD_IO_INFO(&io_info, dset, dxpl_cache, dxpl_id, NULL); + + /* Remove excess chunks */ + if(H5D_istore_prune_by_extent(&io_info, curr_dims) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks ") + + /* Reset the elements outsize the new dimensions, but in existing chunks */ + if(H5D_istore_initialize_by_extent(&io_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks ") + } /* end if */ + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_set_extent() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_flush + * + * Purpose: Flush any dataset information cached in memory + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Ray Lu + * August 14, 2002 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_flush(const H5F_t *f, hid_t dxpl_id, unsigned flags) +{ + hid_t *id_list = NULL; /* Array of dataset IDs */ + unsigned num_dsets; /* Number of datasets in file */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5D_flush, FAIL) + + /* Check args */ + HDassert(f); + + /* Retrieve the # of outstanding dataset IDs */ + num_dsets = H5F_get_obj_count(f, H5F_OBJ_DATASET); + + /* Check for something to do */ + if(num_dsets > 0) { + H5D_t *dataset; /* Dataset pointer */ + unsigned u; /* Index variable */ + + H5_CHECK_OVERFLOW(num_dsets, unsigned, size_t); + if(NULL == (id_list = (hid_t *)H5MM_malloc((size_t)num_dsets * sizeof(hid_t)))) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to allocate memory for ID list") + if(H5F_get_obj_ids(f, H5F_OBJ_DATASET, -1, id_list) != num_dsets) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset ID list") + + /* Iterate through the open datasets */ + for(u = 0; u < num_dsets; u++) { + if(NULL == (dataset = (H5D_t *)H5I_object_verify(id_list[u], H5I_DATASET))) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset object") + + /* Flush the raw data buffer, if we have a dirty one */ + if(dataset->shared->cache.contig.sieve_buf && dataset->shared->cache.contig.sieve_dirty) { + HDassert(dataset->shared->layout.type != H5D_COMPACT); /* We should never have a sieve buffer for compact storage */ + + /* Write dirty data sieve buffer to file */ + if(H5F_block_write(f, H5FD_MEM_DRAW, dataset->shared->cache.contig.sieve_loc, + dataset->shared->cache.contig.sieve_size, dxpl_id, dataset->shared->cache.contig.sieve_buf) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed") + + /* Reset sieve buffer dirty flag */ + dataset->shared->cache.contig.sieve_dirty = FALSE; + } /* end if */ + + /* Flush cached information for each kind of dataset */ + switch(dataset->shared->layout.type) { + case H5D_CONTIGUOUS: + break; + + case H5D_CHUNKED: + /* Flush the raw data cache */ + if(H5D_istore_flush(dataset, dxpl_id, flags & H5F_FLUSH_INVALIDATE) < 0) + HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush raw data cache") + break; + + case H5D_COMPACT: + if(dataset->shared->layout.u.compact.dirty) { + if(H5O_msg_write(&(dataset->oloc), H5O_LAYOUT_ID, 0, H5O_UPDATE_TIME, &(dataset->shared->layout), dxpl_id) < 0) + HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message") + dataset->shared->layout.u.compact.dirty = FALSE; + } /* end if */ + break; + + default: + HDassert("not implemented yet" && 0); +#ifdef NDEBUG + HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout") +#endif /* NDEBUG */ + } /* end switch */ /*lint !e788 All appropriate cases are covered */ + } /* end for */ + } /* end if */ + +done: + if(id_list) + H5MM_xfree(id_list); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_flush() */ + diff --git a/src/H5Dio.c b/src/H5Dio.c index 259eb06..6a6d532 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -1345,7 +1345,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, size_t request_nelmts; /*requested strip mine */ hsize_t smine_start; /*strip mine start loc */ size_t n, smine_nelmts; /*elements per strip */ - size_t accessed_bytes; /*total accessed size in a chunk */ + size_t accessed_bytes = 0; /*total accessed size in a chunk */ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ hbool_t mem_iter_init = FALSE; /*memory selection iteration info has been initialized */ H5S_sel_iter_t bkg_iter; /*background iteration info*/ @@ -2163,7 +2163,7 @@ H5D_compound_opt_read(size_t nelmts, const H5S_t *space, size_t i; H5T_t *src, *dst; - size_t src_stride, dst_stride, type_size; + size_t src_stride, dst_stride, type_size = 0; size_t elmtno; /*element counter */ herr_t ret_value = SUCCEED; /*return value */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index 1f92bf8..cdcc362 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -291,6 +291,18 @@ typedef struct H5D_istore_ud1_t { haddr_t addr; /*file address of chunk */ } H5D_istore_ud1_t; +/* Internal data structure for computing variable-length dataset's total size */ +typedef struct { + hid_t dataset_id; /* ID of the dataset we are working on */ + hid_t fspace_id; /* ID of the file dataset's dataspace we are working on */ + hid_t mspace_id; /* ID of the memory dataset's dataspace we are working on */ + 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 */ + hid_t xfer_pid; /* ID of the dataset xfer property list */ + hsize_t size; /* Accumulated number of bytes for the selection */ +} H5D_vlen_bufsize_t; + + /*****************************/ /* Package Private Variables */ /*****************************/ @@ -306,20 +318,31 @@ H5_DLL H5D_t *H5D_create(H5F_t *file, hid_t type_id, const H5S_t *space, H5_DLL 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); +H5_DLL herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, + hid_t dxpl_id); H5_DLL herr_t H5D_alloc_storage(H5F_t *f, hid_t dxpl_id, H5D_t *dset, H5D_time_alloc_t time_alloc, hbool_t update_time, hbool_t full_overwrite); +H5_DLL hsize_t H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id); +H5_DLL haddr_t H5D_get_offset(const H5D_t *dset); +H5_DLL herr_t H5D_iterate(void *buf, hid_t type_id, const H5S_t *space, + H5D_operator_t op, void *operator_data); +H5_DLL void * H5D_vlen_get_buf_size_alloc(size_t size, void *info); +H5_DLL herr_t H5D_vlen_get_buf_size(void *elem, hid_t type_id, unsigned ndim, + const hsize_t *point, void *op_data); +H5_DLL herr_t H5D_check_filters(H5D_t *dataset); +H5_DLL herr_t H5D_set_extent(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id); /* Functions that perform serial I/O operations */ -H5_DLL herr_t H5D_select_fscat (H5D_io_info_t *io_info, +H5_DLL herr_t H5D_select_fscat(H5D_io_info_t *io_info, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, haddr_t chunk_addr, void *chunk, const void *_buf); -H5_DLL size_t H5D_select_fgath (H5D_io_info_t *io_info, +H5_DLL size_t H5D_select_fgath(H5D_io_info_t *io_info, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, haddr_t chunk_addr, void *chunk, void *buf); -H5_DLL herr_t H5D_select_mscat (const void *_tscat_buf, +H5_DLL herr_t H5D_select_mscat(const void *_tscat_buf, const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts, const H5D_dxpl_cache_t *dxpl_cache, void *_buf/*out*/); -H5_DLL size_t H5D_select_mgath (const void *_buf, +H5_DLL size_t H5D_select_mgath(const void *_buf, const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts, const H5D_dxpl_cache_t *dxpl_cache, void *_tgath_buf/*out*/); H5_DLL herr_t H5D_select_read(H5D_io_info_t *io_info, diff --git a/src/Makefile.am b/src/Makefile.am index ae4950f..fa64fe6 100755 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -46,7 +46,9 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ H5AC.c H5B.c H5Bcache.c \ H5B2.c H5B2cache.c H5B2dbg.c H5B2int.c H5B2stat.c H5B2test.c \ H5C.c H5CS.c \ - H5D.c H5Dcompact.c H5Dcontig.c H5Ddeprec.c H5Defl.c H5Dfill.c H5Dio.c \ + H5D.c H5Dcompact.c H5Dcontig.c H5Ddbg.c \ + H5Ddeprec.c H5Defl.c H5Dfill.c H5Dint.c \ + H5Dio.c \ H5Distore.c H5Dmpio.c H5Doh.c H5Dselect.c H5Dtest.c \ H5E.c H5Edeprec.c H5Eint.c \ H5F.c H5Fdbg.c H5Ffake.c H5Fmount.c H5Fsfile.c H5Fsuper.c H5Ftest.c \ diff --git a/src/Makefile.in b/src/Makefile.in index e83480a..5789b5a 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -83,7 +83,7 @@ am_libhdf5_la_OBJECTS = H5.lo H5checksum.lo H5dbg.lo H5system.lo \ H5Adeprec.lo H5Aint.lo H5Atest.lo H5AC.lo H5B.lo H5Bcache.lo \ H5B2.lo H5B2cache.lo H5B2dbg.lo H5B2int.lo H5B2stat.lo \ H5B2test.lo H5C.lo H5CS.lo H5D.lo H5Dcompact.lo H5Dcontig.lo \ - H5Ddeprec.lo H5Defl.lo H5Dfill.lo H5Dio.lo H5Distore.lo \ + H5Ddbg.lo H5Ddeprec.lo H5Defl.lo H5Dfill.lo H5Dint.lo H5Dio.lo H5Distore.lo \ H5Dmpio.lo H5Doh.lo H5Dselect.lo H5Dtest.lo H5E.lo \ H5Edeprec.lo H5Eint.lo H5F.lo H5Fdbg.lo H5Ffake.lo H5Fmount.lo \ H5Fsfile.lo H5Fsuper.lo H5Ftest.lo H5FD.lo H5FDcore.lo \ @@ -402,7 +402,7 @@ libhdf5_la_SOURCES = H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ H5AC.c H5B.c H5Bcache.c \ H5B2.c H5B2cache.c H5B2dbg.c H5B2int.c H5B2stat.c H5B2test.c \ H5C.c H5CS.c \ - H5D.c H5Dcompact.c H5Dcontig.c H5Ddeprec.c H5Defl.c H5Dfill.c H5Dio.c \ + H5D.c H5Dcompact.c H5Dcontig.c H5Ddbg.c H5Ddeprec.c H5Defl.c H5Dfill.c H5Dint.c H5Dio.c \ H5Distore.c H5Dmpio.c H5Doh.c H5Dselect.c H5Dtest.c \ H5E.c H5Edeprec.c H5Eint.c \ H5F.c H5Fdbg.c H5Ffake.c H5Fmount.c H5Fsfile.c H5Fsuper.c H5Ftest.c \ @@ -598,9 +598,11 @@ distclean-compile: @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5D.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dcompact.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dcontig.Plo@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Ddbg.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Ddeprec.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Defl.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dfill.Plo@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dint.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dio.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Distore.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5Dmpio.Plo@am__quote@ |