/**************************************************************************** * NCSA HDF * * Software Development Group * * National Center for Supercomputing Applications * * University of Illinois at Urbana-Champaign * * 605 E. Springfield, Champaign IL 61820 * * * * For conditions of distribution and use, see the accompanying * * hdf/COPYING file. * * * ****************************************************************************/ /* $Id$ */ #define H5S_PACKAGE /*suppress error about including H5Spkg */ #include "H5private.h" /* Generic Functions */ #include "H5Dprivate.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Gprivate.h" /* Group headers */ #include "H5HLprivate.h" /* Name heap */ #include "H5Iprivate.h" /* IDs */ #include "H5MFprivate.h" /* File space management */ #include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ #include "H5Spkg.h" /* Dataspace functions */ #include "H5Vprivate.h" /* Vector and array functions */ #include "H5Zprivate.h" /* Data filters */ /*#define H5D_DEBUG*/ /* * The MPIO & MPIPOSIX drivers are needed because there are kludges in this * file and places where we check for things that aren't handled by these * drivers. */ #include "H5FDmpio.h" #include "H5FDmpiposix.h" #ifdef H5_HAVE_PARALLEL /* Remove this if H5R_DATASET_REGION is no longer used in this file */ # include "H5Rpublic.h" #endif /*H5_HAVE_PARALLEL*/ /* Pablo information */ #define PABLO_MASK H5D_mask /* Local typedefs */ /* * A dataset is the following struct. */ struct H5D_t { H5G_entry_t ent; /* cached object header stuff */ H5T_t *type; /* datatype of this dataset */ hid_t dcpl_id; /* dataset creation property id */ H5O_layout_t layout; /* data layout */ }; /* Enumerated type for allocating dataset's storage */ typedef enum { H5D_ALLOC_CREATE, /* Dataset is being created */ H5D_ALLOC_OPEN, /* Dataset is being opened */ H5D_ALLOC_EXTEND, /* Dataset's dataspace is being extended */ H5D_ALLOC_WRITE /* Dataset is being extended */ } H5D_time_alloc_t; /* Interface initialization */ static int interface_initialize_g = 0; #define INTERFACE_INIT H5D_init_interface /* Local functions */ static herr_t H5D_init_interface(void); static herr_t H5D_alloc_storage (H5F_t *f, H5D_t *dset,H5D_time_alloc_t time_alloc); static herr_t H5D_init_storage(H5D_t *dataset); H5D_t * H5D_new(hid_t dcpl_id); static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space); static herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation); /* Declare a free list to manage the H5D_t struct */ H5FL_DEFINE_STATIC(H5D_t); /* Declare a free list to manage blocks of type conversion data */ H5FL_BLK_DEFINE(type_conv); /* Declare a free list to manage blocks of single datatype element data */ H5FL_BLK_DEFINE(type_elem); /* 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); /*------------------------------------------------------------------------- * Function: H5D_init * * Purpose: Initialize the interface from some other layer. * * Return: Success: non-negative * * Failure: negative * * Programmer: Quincey Koziol * Saturday, March 4, 2000 * * Modifications: * *------------------------------------------------------------------------- */ 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(ret_value); } /*-------------------------------------------------------------------------- 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) { /* Dataset Transfer property class variables. In sequence, they are, * - Transfer Property list class to modify * - Default value for maximum temp buffer size * - Default value for type conversion buffer * - Default value for background buffer * - Default value for B-tree node split ratios * - Default value for hyperslab caching * - Default value for hyperslab cache limit * - Default value for vlen allocation function * - Default value for vlen allocation information * - Default value for vlen free function * - Default value for vlen free information * - Default value for file driver ID * - Default value for file driver info * - Default value for 'gather reads' property * - Default value for vector size */ H5P_genclass_t *xfer_pclass; size_t def_max_temp_buf = H5D_XFER_MAX_TEMP_BUF_DEF; void *def_tconv_buf = H5D_XFER_TCONV_BUF_DEF; void *def_bkgr_buf = H5D_XFER_BKGR_BUF_DEF; H5T_bkg_t def_bkgr_buf_type = H5D_XFER_BKGR_BUF_TYPE_DEF; double def_btree_split_ratio[3] = H5D_XFER_BTREE_SPLIT_RATIO_DEF; #ifdef H5_WANT_H5_V1_4_COMPAT unsigned def_hyper_cache = H5D_XFER_HYPER_CACHE_DEF; unsigned def_hyper_cache_lim = H5D_XFER_HYPER_CACHE_LIM_DEF; #endif /* H5_WANT_H5_V1_4_COMPAT */ H5MM_allocate_t def_vlen_alloc = H5D_XFER_VLEN_ALLOC_DEF; void *def_vlen_alloc_info = H5D_XFER_VLEN_ALLOC_INFO_DEF; H5MM_free_t def_vlen_free = H5D_XFER_VLEN_FREE_DEF; void *def_vlen_free_info = H5D_XFER_VLEN_FREE_INFO_DEF; hid_t def_vfl_id = H5D_XFER_VFL_ID_DEF; void *def_vfl_info = H5D_XFER_VFL_INFO_DEF; size_t def_hyp_vec_size = H5D_XFER_HYPER_VECTOR_SIZE_DEF; /* Dataset creation property class variables. In sequence, they are, * - Creation property list class to modify * - Default value for storage layout property * - Default value for chunk dimensionality property * - Default value for chunk size * - Default value for fill value * - Default value for external file list * - Default value for data filter pipeline */ H5P_genclass_t *crt_pclass; H5D_layout_t layout = H5D_CRT_LAYOUT_DEF; int chunk_ndims = H5D_CRT_CHUNK_DIM_DEF; hsize_t chunk_size[32] = H5D_CRT_CHUNK_SIZE_DEF; H5O_fill_t fill = H5D_CRT_FILL_VALUE_DEF; H5D_alloc_time_t alloc_time = H5D_CRT_ALLOC_TIME_DEF; H5D_fill_time_t fill_time = H5D_CRT_FILL_TIME_DEF; H5O_efl_t efl = H5D_CRT_EXT_FILE_LIST_DEF; H5O_pline_t pline = H5D_CRT_DATA_PIPELINE_DEF; size_t nprops; /* Number of properties */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_init_interface); /* Initialize the atom group for the dataset IDs */ if (H5I_init_group(H5I_DATASET, H5I_DATASETID_HASHSIZE, H5D_RESERVED_ATOMS, (H5I_free_t)H5D_close)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize interface"); /* =========Dataset Transfer Property Class Initialization========= */ /* Register the default dataset transfer properties */ assert(H5P_CLS_DATASET_XFER_g!=(-1)); /* Get the pointer to the dataset transfer class */ if (NULL == (xfer_pclass = H5I_object_verify(H5P_CLS_DATASET_XFER_g, H5I_GENPROP_CLS))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list class"); /* Get the number of properties in the class */ if(H5P_get_nprops_pclass(xfer_pclass,&nprops)<0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "can't query number of properties"); /* Assume that if there are properties in the class, they are the default ones */ if(nprops==0) { /* Register the max. temp buffer size property */ if(H5P_register(xfer_pclass,H5D_XFER_MAX_TEMP_BUF_NAME,H5D_XFER_MAX_TEMP_BUF_SIZE,&def_max_temp_buf,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the type conversion buffer property */ if(H5P_register(xfer_pclass,H5D_XFER_TCONV_BUF_NAME,H5D_XFER_TCONV_BUF_SIZE,&def_tconv_buf,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the background buffer property */ if(H5P_register(xfer_pclass,H5D_XFER_BKGR_BUF_NAME,H5D_XFER_BKGR_BUF_SIZE,&def_bkgr_buf,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the background buffer type property */ if(H5P_register(xfer_pclass,H5D_XFER_BKGR_BUF_TYPE_NAME,H5D_XFER_BKGR_BUF_TYPE_SIZE,&def_bkgr_buf_type,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the B-Tree node splitting ratios property */ if(H5P_register(xfer_pclass,H5D_XFER_BTREE_SPLIT_RATIO_NAME,H5D_XFER_BTREE_SPLIT_RATIO_SIZE,&def_btree_split_ratio,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); #ifdef H5_WANT_H5_V1_4_COMPAT /* Register the hyperslab caching property */ if(H5P_register(xfer_pclass,H5D_XFER_HYPER_CACHE_NAME,H5D_XFER_HYPER_CACHE_SIZE,&def_hyper_cache,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the hyperslab cache limit property */ if(H5P_register(xfer_pclass,H5D_XFER_HYPER_CACHE_LIM_NAME,H5D_XFER_HYPER_CACHE_LIM_SIZE,&def_hyper_cache_lim,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); #endif /* H5_WANT_H5_V1_4_COMPAT */ /* Register the vlen allocation function property */ if(H5P_register(xfer_pclass,H5D_XFER_VLEN_ALLOC_NAME,H5D_XFER_VLEN_ALLOC_SIZE,&def_vlen_alloc,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the vlen allocation information property */ if(H5P_register(xfer_pclass,H5D_XFER_VLEN_ALLOC_INFO_NAME,H5D_XFER_VLEN_ALLOC_INFO_SIZE,&def_vlen_alloc_info,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the vlen free function property */ if(H5P_register(xfer_pclass,H5D_XFER_VLEN_FREE_NAME,H5D_XFER_VLEN_FREE_SIZE,&def_vlen_free,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the vlen free information property */ if(H5P_register(xfer_pclass,H5D_XFER_VLEN_FREE_INFO_NAME,H5D_XFER_VLEN_FREE_INFO_SIZE,&def_vlen_free_info,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the file driver ID property */ if(H5P_register(xfer_pclass,H5D_XFER_VFL_ID_NAME,H5D_XFER_VFL_ID_SIZE,&def_vfl_id,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the file driver info property */ if(H5P_register(xfer_pclass,H5D_XFER_VFL_INFO_NAME,H5D_XFER_VFL_INFO_SIZE,&def_vfl_info,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the vector size property */ if(H5P_register(xfer_pclass,H5D_XFER_HYPER_VECTOR_SIZE_NAME,H5D_XFER_HYPER_VECTOR_SIZE_SIZE,&def_hyp_vec_size,NULL,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); } /* end if */ /* Only register the default property list if it hasn't been created yet */ if(H5P_LST_DATASET_XFER_g==(-1)) { /* Register the default data transfer property list */ if ((H5P_LST_DATASET_XFER_g = H5P_create_id (xfer_pclass))<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTREGISTER, FAIL, "can't register default property list"); } /* end if */ /* =========Dataset Creation Property Class Initialization========== */ /* Register the default dataset creation properties */ assert(H5P_CLS_DATASET_CREATE_g != -1); /* Get the pointer to the dataset creation class */ if(NULL == (crt_pclass = H5I_object_verify(H5P_CLS_DATASET_CREATE_g, H5I_GENPROP_CLS))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list class"); /* Get the number of properties in the class */ if(H5P_get_nprops_pclass(crt_pclass,&nprops)<0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "can't query number of properties"); /* Assume that if there are properties in the class, they are the default ones */ if(nprops==0) { /* Register the storage layout property */ if(H5P_register(crt_pclass, H5D_CRT_LAYOUT_NAME, H5D_CRT_LAYOUT_SIZE, &layout, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the chunking dimensionality property */ if(H5P_register(crt_pclass, H5D_CRT_CHUNK_DIM_NAME, H5D_CRT_CHUNK_DIM_SIZE, &chunk_ndims, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the chunking size property */ if(H5P_register(crt_pclass, H5D_CRT_CHUNK_SIZE_NAME, H5D_CRT_CHUNK_SIZE_SIZE, chunk_size, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the fill value property */ if(H5P_register(crt_pclass, H5D_CRT_FILL_VALUE_NAME, H5D_CRT_FILL_VALUE_SIZE, &fill, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the space allocation time property */ if(H5P_register(crt_pclass, H5D_CRT_ALLOC_TIME_NAME, H5D_CRT_ALLOC_TIME_SIZE, &alloc_time, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the fill value writing time property */ if(H5P_register(crt_pclass, H5D_CRT_FILL_TIME_NAME, H5D_CRT_FILL_TIME_SIZE, &fill_time, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the external file list property */ if(H5P_register(crt_pclass, H5D_CRT_EXT_FILE_LIST_NAME, H5D_CRT_EXT_FILE_LIST_SIZE, &efl, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); /* Register the data pipeline property */ if(H5P_register(crt_pclass, H5D_CRT_DATA_PIPELINE_NAME, H5D_CRT_DATA_PIPELINE_SIZE, &pline, NULL, NULL, NULL, NULL, NULL, NULL) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); } /* end if */ /* Only register the default property list if it hasn't been created yet */ if(H5P_LST_DATASET_CREATE_g==(-1)) { /* Register the default data transfer property list */ if ((H5P_LST_DATASET_CREATE_g = H5P_create_id (crt_pclass))<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTREGISTER, FAIL, "can't register default property list"); } /* end if */ done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * 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 * * Modifications: * *------------------------------------------------------------------------- */ int H5D_term_interface(void) { int n=0; FUNC_ENTER_NOINIT(H5D_term_interface); if (interface_initialize_g) { if ((n=H5I_nmembers(H5I_DATASET))) { H5I_clear_group(H5I_DATASET, FALSE); } else { H5I_destroy_group(H5I_DATASET); interface_initialize_g = 0; n = 1; /*H5I*/ } } FUNC_LEAVE(n); } /*------------------------------------------------------------------------- * Function: H5D_crt_copy * * Purpose: Callback routine which is called whenever any dataset * creation property list is copied. This routine copies * the properties from the old list to the new list. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Raymond Lu * Tuesday, October 2, 2001 * * Modification: * *------------------------------------------------------------------------- */ herr_t H5D_crt_copy(hid_t new_plist_id, hid_t old_plist_id, void UNUSED *copy_data) { H5O_fill_t src_fill, dst_fill; H5O_efl_t src_efl, dst_efl; H5O_pline_t src_pline, dst_pline; H5P_genplist_t *old_plist; H5P_genplist_t *new_plist; herr_t ret_value=SUCCEED; FUNC_ENTER_NOAPI(H5D_crt_copy, FAIL); /* Verify property list ID */ if (NULL == (new_plist = H5P_object_verify(new_plist_id,H5P_DATASET_CREATE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if (NULL == (old_plist = H5P_object_verify(old_plist_id,H5P_DATASET_CREATE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the fill value, external file list, and data pipeline properties * from the old property list */ HDmemset(&src_fill,0,sizeof(H5O_fill_t)); if(H5P_get(old_plist, H5D_CRT_FILL_VALUE_NAME, &src_fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get fill value"); HDmemset(&src_efl,0,sizeof(H5O_efl_t)); if(H5P_get(old_plist, H5D_CRT_EXT_FILE_LIST_NAME, &src_efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file list"); HDmemset(&src_pline,0,sizeof(H5O_pline_t)); if(H5P_get(old_plist, H5D_CRT_DATA_PIPELINE_NAME, &src_pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get pipeline"); /* Make copies of fill value, external file list, and data pipeline */ HDmemset(&dst_fill,0,sizeof(H5O_fill_t)); if(src_fill.buf && (NULL==H5O_copy(H5O_FILL, &src_fill, &dst_fill))) { HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy fill value"); } else if (!src_fill.buf) { dst_fill.type = dst_fill.buf = NULL; dst_fill.size = src_fill.size; } HDmemset(&dst_efl,0,sizeof(H5O_efl_t)); if(NULL==H5O_copy(H5O_EFL, &src_efl, &dst_efl)) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy external file list"); HDmemset(&dst_pline,0,sizeof(H5O_pline_t)); if(NULL==H5O_copy(H5O_PLINE, &src_pline, &dst_pline)) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy data pipeline"); /* Set the fill value, external file list, and data pipeline property * for the new property list */ if(H5P_set(new_plist, H5D_CRT_FILL_VALUE_NAME, &dst_fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set fill value"); if(H5P_set(new_plist, H5D_CRT_EXT_FILE_LIST_NAME, &dst_efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set external file list"); if(H5P_set(new_plist, H5D_CRT_DATA_PIPELINE_NAME, &dst_pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set pipeline"); done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_crt_close * * Purpose: Callback routine which is called whenever any dataset create * property list is closed. This routine performs any generic * cleanup needed on the properties the library put into the list. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Quincey Koziol * Wednesday, July 11, 2001 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_crt_close(hid_t dcpl_id, void UNUSED *close_data) { H5O_fill_t fill; H5O_efl_t efl; H5O_pline_t pline; H5P_genplist_t *plist; /* Property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_crt_close, FAIL); /* Check arguments */ if (NULL == (plist = H5P_object_verify(dcpl_id,H5P_DATASET_CREATE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the fill value, external file list, and data pipeline properties * from the old property list */ HDmemset(&fill,0,sizeof(H5O_fill_t)); if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get fill value"); HDmemset(&efl,0,sizeof(H5O_efl_t)); if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file list"); HDmemset(&pline,0,sizeof(H5O_pline_t)); if(H5P_get(plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get pipeline"); /* Clean up any values set for the fill-value, external file-list and * data pipeline */ H5O_reset(H5O_FILL, &fill); H5O_reset(H5O_EFL, &efl); H5O_reset(H5O_PLINE, &pline); done: FUNC_LEAVE(ret_value); } /* end H5D_crt_close() */ /*------------------------------------------------------------------------- * Function: H5D_xfer_create * * Purpose: Callback routine which is called whenever any dataset transfer * property list is created. This routine performs any generic * initialization needed on the properties the library put into * the list. * Right now, it's just allocating the driver-specific dataset * transfer information. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Quincey Koziol * Thursday, August 2, 2001 * * Notes: This same routine is currently used for the 'copy' callback. * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_xfer_create(hid_t dxpl_id, void UNUSED *create_data) { hid_t driver_id; /* VFL driver ID */ void *driver_info; /* VFL driver info */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_xfer_create, FAIL); /* Check arguments */ if (NULL == (plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list"); /* Get the driver information */ if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID"); if(H5P_get(plist, H5D_XFER_VFL_INFO_NAME, &driver_info)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver info"); /* Check if we have a valid driver ID */ if(driver_id>0) { /* Increment the reference count on the driver and copy the driver info */ if(H5I_inc_ref(driver_id)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINC, FAIL, "Can't increment VFL driver ID"); if((driver_info = H5FD_dxpl_copy(driver_id, driver_info))==NULL) HGOTO_ERROR (H5E_DATASET, H5E_CANTCOPY, FAIL, "Can't copy VFL driver"); /* Set the driver information for the new property list */ if(H5P_set(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTSET, FAIL, "Can't set VFL driver ID"); if(H5P_set(plist, H5D_XFER_VFL_INFO_NAME, &driver_info)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTSET, FAIL, "Can't set VFL driver info"); } /* end if */ done: FUNC_LEAVE(ret_value); } /* end H5D_xfer_create() */ /*------------------------------------------------------------------------- * Function: H5D_xfer_copy * * Purpose: Callback routine which is called whenever any dataset * transfer property list is copied. This routine copies * the properties from the old list to the new list. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Raymond Lu * Tuesday, October 2, 2001 * * Modification: * *------------------------------------------------------------------------- */ herr_t H5D_xfer_copy(hid_t new_plist_id, hid_t UNUSED old_plist_id, void *copy_data) { herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_xfer_copy, FAIL); if(H5D_xfer_create(new_plist_id, copy_data) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't copy property list"); done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_xfer_close * * Purpose: Callback routine which is called whenever any dataset transfer * property list is closed. This routine performs any generic * cleanup needed on the properties the library put into the list. * Right now, it's just freeing the driver-specific dataset * transfer information. * * Return: Success: Non-negative * * Failure: Negative * * Programmer: Quincey Koziol * Wednesday, July 11, 2001 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_xfer_close(hid_t dxpl_id, void UNUSED *close_data) { hid_t driver_id; /* VFL driver ID */ void *driver_info; /* VFL driver info */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_xfer_close, FAIL); /* Check arguments */ if (NULL == (plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list"); if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID"); if(H5P_get(plist, H5D_XFER_VFL_INFO_NAME, &driver_info)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver info"); if(driver_id>0) { if(H5FD_dxpl_free(driver_id, driver_info)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't free VFL driver"); if(H5I_dec_ref(driver_id)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement VFL driver ID"); } /* end if */ done: FUNC_LEAVE(ret_value); } /* end H5D_xfer_close() */ /*------------------------------------------------------------------------- * Function: H5Dcreate * * Purpose: Creates a new dataset named NAME at LOC_ID, opens the * dataset for access, and associates with that dataset constant * and initial persistent properties including the type of each * datapoint as stored in the file (TYPE_ID), the size of the * dataset (SPACE_ID), and other initial miscellaneous * properties (PLIST_ID). * * All arguments are copied into the dataset, so the caller is * allowed to derive new types, data spaces, and creation * parameters from the old ones and reuse them in calls to * create other datasets. * * Return: Success: The object ID of the new dataset. At this * point, the dataset is ready to receive its * raw data. Attempting to read raw data from * the dataset will probably return the fill * value. The dataset should be closed when * the caller is no longer interested in it. * * Failure: FAIL * * Errors: * ARGS BADTYPE Not a data space. * ARGS BADTYPE Not a dataset creation plist. * ARGS BADTYPE Not a file. * ARGS BADTYPE Not a type. * ARGS BADVALUE No name. * DATASET CANTINIT Can't create dataset. * DATASET CANTREGISTER Can't register dataset. * * Programmer: Robb Matzke * Wednesday, December 3, 1997 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5Dcreate(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t plist_id) { H5G_entry_t *loc = NULL; H5T_t *type = NULL; H5S_t *space = NULL; H5D_t *new_dset = NULL; hid_t ret_value; FUNC_ENTER_API(H5Dcreate, FAIL); H5TRACE5("i","isiii",loc_id,name,type_id,space_id,plist_id); /* Check arguments */ if (NULL == (loc = H5G_loc(loc_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location"); if (!name || !*name) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name"); if (NULL == (type = H5I_object_verify(type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a type"); if (NULL == (space = H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); if(H5P_DEFAULT == plist_id) plist_id = H5P_DATASET_CREATE_DEFAULT; if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_CREATE)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not dataset create property list"); /* build and open the new dataset */ if (NULL == (new_dset = H5D_create(loc, name, type, space, plist_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset"); /* Register the new dataset to get an ID for it */ if ((ret_value = H5I_register(H5I_DATASET, new_dset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataset"); done: if(ret_value<0) { if(new_dset!=NULL) H5D_close(new_dset); } /* end if */ FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dopen * * Purpose: Finds a dataset named NAME at LOC_ID, opens it, and returns * its ID. The dataset should be close when the caller is no * longer interested in it. * * Return: Success: A new dataset ID * * Failure: FAIL * * Errors: * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5Dopen(hid_t loc_id, const char *name) { H5G_entry_t *loc = NULL; /*location holding the dataset */ H5D_t *dataset = NULL; /*the dataset */ hid_t ret_value; FUNC_ENTER_API(H5Dopen, FAIL); H5TRACE2("i","is",loc_id,name); /* Check args */ if (NULL == (loc = H5G_loc(loc_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location"); if (!name || !*name) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name"); /* Find the dataset */ if (NULL == (dataset = H5D_open(loc, name))) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "dataset not found"); /* Create an atom for the dataset */ if ((ret_value = H5I_register(H5I_DATASET, dataset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register dataset"); done: if(ret_value<0) { if(dataset!=NULL) H5D_close(dataset); } /* end if */ FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dclose * * Purpose: Closes access to a dataset (DATASET_ID) and releases * resources used by it. It is illegal to subsequently use that * same dataset ID in calls to other dataset functions. * * Return: Non-negative on success/Negative on failure * * Errors: * ARGS BADTYPE Not a dataset. * DATASET CANTINIT Can't free. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dclose(hid_t dset_id) { H5D_t *dset = NULL; /* Dataset object to release */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dclose, FAIL); H5TRACE1("e","i",dset_id); /* Check args */ if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == dset->ent.file) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not a dataset"); /* * Decrement the counter on the dataset. It will be freed if the count * reaches zero. */ if (H5I_dec_ref(dset_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't free"); done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dget_space * * Purpose: Returns a copy of the file data space for a dataset. * * Return: Success: ID for a copy of the data space. The data * space should be released by calling * H5Sclose(). * * Failure: FAIL * * Programmer: Robb Matzke * Wednesday, January 28, 1998 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space is not constant and is no longer cached by the dataset * struct. *------------------------------------------------------------------------- */ hid_t H5Dget_space(hid_t dset_id) { H5D_t *dset = NULL; H5S_t *space = NULL; hid_t ret_value; FUNC_ENTER_API(H5Dget_space, FAIL); H5TRACE1("i","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); /* Read the data space message and return a data space object */ if (NULL==(space=H5D_get_space (dset))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get data space"); /* Create an atom */ if ((ret_value=H5I_register (H5I_DATASPACE, space))<0) HGOTO_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register data space"); done: if(ret_value<0) { if(space!=NULL) H5S_close(space); } /* end if */ FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5D_get_space * * Purpose: Returns the data space associated with the dataset. * * Return: Success: Ptr to a copy of the data space. * * Failure: NULL * * Programmer: Robb Matzke * Tuesday, August 25, 1998 * * Modifications: * *------------------------------------------------------------------------- */ H5S_t * H5D_get_space(H5D_t *dset) { H5S_t *space; H5S_t *ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_get_space, NULL); assert(dset); if (NULL==(space=H5S_read(&(dset->ent)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load space info from dataset header"); /* Set return value */ ret_value=space; done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dget_space_status * * Purpose: Returns the status of data space allocation. * * Return: * Success: Non-negative * * Failture: Negative * * Programmer: Raymond Lu * * Modification: * *------------------------------------------------------------------------- */ herr_t H5Dget_space_status(hid_t dset_id, H5D_space_status_t *allocation) { H5D_t *dset = NULL; herr_t ret_value = SUCCEED; FUNC_ENTER_API(H5Dget_space_status, FAIL); /* Check arguments */ if(NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); /* Read data space address and return */ if(FAIL==(ret_value=H5D_get_space_status(dset, allocation))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get space status"); done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_get_space_status * * Purpose: Returns the status of data space allocation. * * Return: * Success: Non-negative * * Failture: Negative * * Programmer: Raymond Lu * * Modification: * *------------------------------------------------------------------------- */ static herr_t H5D_get_space_status(H5D_t *dset, H5D_space_status_t *allocation) { H5S_t *space=NULL; /* 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_NOINIT(H5D_get_space_status); /* Get the dataset's dataspace */ if((space=H5D_get_space(dset))==NULL) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get dataspace"); /* Get the total number of elements in dataset's dataspace */ if((total_elem=H5S_get_simple_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->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); /* 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 */ assert(dset->layout.type==H5D_CHUNKED); *allocation = H5D_SPACE_STATUS_PART_ALLOCATED; } /* end else */ done: if(space) H5S_close(space); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dget_type * * Purpose: Returns a copy of the file data type for a dataset. * * Return: Success: ID for a copy of the data type. The data * type should be released by calling * H5Tclose(). * * Failure: FAIL * * Programmer: Robb Matzke * Tuesday, February 3, 1998 * * Modifications: * * Robb Matzke, 1 Jun 1998 * If the dataset has a named data type then a handle to the opened data * type is returned. Otherwise the returned data type is read-only. If * atomization of the data type fails then the data type is closed. * *------------------------------------------------------------------------- */ hid_t H5Dget_type(hid_t dset_id) { H5D_t *dset = NULL; H5T_t *copied_type = NULL; hid_t ret_value = FAIL; FUNC_ENTER_API(H5Dget_type, FAIL); H5TRACE1("i","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); /* Copy the data type and mark it read-only */ if (NULL==(copied_type=H5T_copy (dset->type, H5T_COPY_REOPEN))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy the data type"); /* Mark any VL datatypes as being in memory now */ if (H5T_vlen_mark(copied_type, NULL, H5T_VLEN_MEMORY)<0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid VL location"); /* Unlock copied type */ if (H5T_lock (copied_type, FALSE)<0) HGOTO_ERROR (H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to lock transient data type"); /* Create an atom */ if ((ret_value=H5I_register (H5I_DATATYPE, copied_type))<0) HGOTO_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register data type"); done: if(ret_value<0) { if(copied_type!=NULL) H5T_close (copied_type); } /* end if */ FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5Dget_create_plist * * Purpose: Returns a copy of the dataset creation property list. * * Return: Success: ID for a copy of the dataset creation * property list. The template should be * released by calling H5P_close(). * * Failure: FAIL * * Programmer: Robb Matzke * Tuesday, February 3, 1998 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * The way to retrieve and set property is changed for the * generic property list. * *------------------------------------------------------------------------- */ hid_t H5Dget_create_plist(hid_t dset_id) { H5D_t *dset = NULL; H5O_fill_t copied_fill={NULL,0,NULL}; H5P_genplist_t *dcpl_plist; H5P_genplist_t *new_plist; hid_t new_dcpl_id = FAIL; hid_t ret_value = FAIL; FUNC_ENTER_API(H5Dget_create_plist, FAIL); H5TRACE1("i","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == (dcpl_plist = H5I_object(dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get property list"); /* Copy the creation property list */ if((new_dcpl_id = H5P_copy_plist(dcpl_plist)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to copy the creation property list"); if (NULL == (new_plist = H5I_object(new_dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get property list"); /* Get the fill value property */ if(H5P_get(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get fill value"); /* Copy the dataset type into the fill value message */ if(copied_fill.type==NULL) if(NULL==(copied_fill.type=H5T_copy(dset->type, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy dataset data type for fill value"); /* Set back the fill value property to property list */ if(H5P_set(new_plist, H5D_CRT_FILL_VALUE_NAME, &copied_fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property list fill value"); /* Set the return value */ ret_value=new_dcpl_id; done: if(ret_value<0) { if(new_dcpl_id>0) H5Pclose(new_dcpl_id); } /* end if */ FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5Dread * * Purpose: Reads (part of) a DSET from the file into application * memory BUF. The part of the dataset to read is defined with * MEM_SPACE_ID and FILE_SPACE_ID. The data points are * converted from their file type to the MEM_TYPE_ID specified. * Additional miscellaneous data transfer properties can be * passed to this function with the PLIST_ID argument. * * The FILE_SPACE_ID can be the constant H5S_ALL which indicates * that the entire file data space is to be referenced. * * The MEM_SPACE_ID can be the constant H5S_ALL in which case * the memory data space is the same as the file data space * defined when the dataset was created. * * The number of elements in the memory data space must match * the number of elements in the file data space. * * The PLIST_ID can be the constant H5P_DEFAULT in which * case the default data transfer properties are used. * * Return: Non-negative on success/Negative on failure * * Errors: * ARGS BADTYPE Not a data space. * ARGS BADTYPE Not a data type. * ARGS BADTYPE Not a dataset. * ARGS BADTYPE Not xfer parms. * ARGS BADVALUE No output buffer. * DATASET READERROR Can't read data. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, void *buf/*out*/) { H5D_t *dset = NULL; const H5T_t *mem_type = NULL; const H5S_t *mem_space = NULL; const H5S_t *file_space = NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dread, FAIL); H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id, plist_id,buf); /* check arguments */ if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == dset->ent.file) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); if (H5S_ALL != mem_space_id) { if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); /* Check for valid selection */ if((*mem_space->select.is_valid)(mem_space)!=TRUE) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } if (H5S_ALL != file_space_id) { if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); /* Check for valid selection */ if((*file_space->select.is_valid)(file_space)!=TRUE) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == plist_id) plist_id= H5P_DATASET_XFER_DEFAULT; if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); if (!buf) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); /* read raw data */ if (H5D_read(dset, mem_type, mem_space, file_space, plist_id, buf/*out*/) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data"); done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dwrite * * Purpose: Writes (part of) a DSET from application memory BUF to the * file. The part of the dataset to write is defined with the * MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points * are converted from their current type (MEM_TYPE_ID) to their * file data type. Additional miscellaneous data transfer * properties can be passed to this function with the * PLIST_ID argument. * * The FILE_SPACE_ID can be the constant H5S_ALL which indicates * that the entire file data space is to be referenced. * * The MEM_SPACE_ID can be the constant H5S_ALL in which case * the memory data space is the same as the file data space * defined when the dataset was created. * * The number of elements in the memory data space must match * the number of elements in the file data space. * * The PLIST_ID can be the constant H5P_DEFAULT in which * case the default data transfer properties are used. * * Return: Non-negative on success/Negative on failure * * Errors: * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, const void *buf) { H5D_t *dset = NULL; const H5T_t *mem_type = NULL; const H5S_t *mem_space = NULL; const H5S_t *file_space = NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dwrite, FAIL); H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id, plist_id,buf); /* check arguments */ if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == dset->ent.file) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); if (H5S_ALL != mem_space_id) { if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); /* Check for valid selection */ if ((*mem_space->select.is_valid)(mem_space)!=TRUE) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } if (H5S_ALL != file_space_id) { if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); /* Check for valid selection */ if ((*file_space->select.is_valid)(file_space)!=TRUE) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == plist_id) plist_id= H5P_DATASET_XFER_DEFAULT; if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); if (!buf) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); /* write raw data */ if (H5D_write(dset, mem_type, mem_space, file_space, plist_id, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data"); done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dextend * * Purpose: This function makes sure that the dataset is at least of size * SIZE. The dimensionality of SIZE is the same as the data * space of the dataset being changed. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Friday, January 30, 1998 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dextend(hid_t dset_id, const hsize_t *size) { H5D_t *dset = NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dextend, FAIL); H5TRACE2("e","i*h",dset_id,size); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (!size) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified"); /* Increase size */ if (H5D_extend (dset, size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to extend dataset"); done: FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5D_new * * Purpose: Creates a new, empty dataset structure * * Return: Success: Pointer to a new dataset descriptor. * * Failure: NULL * * Errors: * * Programmer: Quincey Koziol * Monday, October 12, 1998 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to query and inialization for generic * property list. * *------------------------------------------------------------------------- */ H5D_t * H5D_new(hid_t dcpl_id) { H5P_genplist_t *plist; /* Property list created */ H5D_t *new_dset = NULL; /* New dataset object */ H5D_t *ret_value; /* Return value */ FUNC_ENTER_NOAPI(H5D_new, NULL); if (NULL==(new_dset = H5FL_ALLOC(H5D_t,1))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); if(H5P_DEFAULT == dcpl_id) dcpl_id = H5P_DATASET_CREATE_DEFAULT; /* Get the property list */ if (NULL == (plist = H5P_object_verify(dcpl_id,H5P_DATASET_CREATE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list"); new_dset->dcpl_id = H5P_copy_plist(plist); new_dset->ent.header = HADDR_UNDEF; /* Set return value */ ret_value=new_dset; done: if(ret_value==NULL) { if(new_dset!=NULL) H5FL_FREE(H5D_t,new_dset); } /* end if */ FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * 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 * * Errors: * DATASET CANTINIT Can't update dataset header. * DATASET CANTINIT Problem with the dataset name. * DATASET CANTINIT Fail in file space allocation for * chunks * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space message is no longer cached in the dataset struct. * * Robb Matzke, 27 Jul 1998 * Added the MTIME message to the dataset object header. * * Robb Matzke, 1999-10-14 * The names for the external file list are entered into the heap hear * instead of when the efl message is encoded, preventing a possible * infinite recursion situation. * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to retrieve and set property for generic property * list. * * Raymond Lu, 26 Feb 2002 * A new fill value message is added. Two properties, space allocation * time and fill value writing time, govern space allocation and fill * value writing. * *------------------------------------------------------------------------- */ H5D_t * H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, const H5S_t *space, hid_t dcpl_id) { H5D_t *new_dset = NULL; H5D_t *ret_value = NULL; int i, ndims; hsize_t comp_data_size; unsigned u; hsize_t max_dim[H5O_LAYOUT_NDIMS]={0}; H5O_efl_t efl; H5F_t *f = NULL; H5O_pline_t dcpl_pline; H5D_layout_t dcpl_layout; int chunk_ndims = 0; hsize_t chunk_size[32]={0}; H5D_alloc_time_t alloc_time; H5D_fill_time_t fill_time; H5O_fill_t fill_prop={NULL,0,NULL}; H5O_fill_new_t fill={NULL, 0, NULL, H5D_ALLOC_TIME_LATE, H5D_FILL_TIME_ALLOC, TRUE}; H5D_fill_value_t fill_status; H5P_genplist_t *plist; /* Property list */ H5P_genplist_t *new_plist; /* New Property list */ FUNC_ENTER_NOAPI(H5D_create, NULL); /* check args */ assert (loc); assert (name && *name); assert (type); assert (space); /* Get property list object */ if (NULL == (plist = H5P_object_verify(dcpl_id,H5P_DATASET_CREATE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list"); if(H5P_get(plist, H5D_CRT_DATA_PIPELINE_NAME, &dcpl_pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve pipeline filter"); if(H5P_get(plist, H5D_CRT_LAYOUT_NAME, &dcpl_layout) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); if(dcpl_pline.nfilters > 0 && H5D_CHUNKED != dcpl_layout) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "filters can only be used with chunked layout"); if(H5P_get(plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); /* Check if the alloc_time is the default and set it accordingly */ if(alloc_time==H5D_ALLOC_TIME_DEFAULT) { switch(dcpl_layout) { case H5D_COMPACT: alloc_time=H5D_ALLOC_TIME_EARLY; break; case H5D_CONTIGUOUS: alloc_time=H5D_ALLOC_TIME_LATE; break; case H5D_CHUNKED: alloc_time=H5D_ALLOC_TIME_INCR; break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* end switch */ } /* end if */ /* Don't allow compact datasets to allocate space later */ if(dcpl_layout==H5D_COMPACT && alloc_time!=H5D_ALLOC_TIME_EARLY) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "compact dataset doesn't support late space allocation"); /* What file is the dataset being added to? */ if (NULL==(f=H5G_insertion_file(loc, name))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to locate insertion point"); /* If MPIO or MPIPOSIX is used, no filter support yet. */ if((IS_H5FD_MPIO(f) || IS_H5FD_MPIPOSIX(f)) && dcpl_pline.nfilters > 0) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel I/O does not support filters yet"); /* Check if this dataset is going into a parallel file and set space allocation time */ if(IS_H5FD_MPIO(f) || IS_H5FD_MPIPOSIX(f)) alloc_time=H5D_ALLOC_TIME_EARLY; if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill time"); if(fill_time==H5D_FILL_TIME_NEVER && H5T_detect_class(type, H5T_VLEN)) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "Dataset doesn't support VL datatype when fill value is not defined"); /* Initialize the dataset object */ if(NULL == (new_dset = H5D_new(dcpl_id))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); /* 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"); /* Copy datatype for dataset */ if((new_dset->type = H5T_copy(type, H5T_COPY_ALL))==NULL) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, NULL, "can't copy datatype"); /* Mark any VL datatypes as being on disk now */ if (H5T_vlen_mark(new_dset->type, f, H5T_VLEN_DISK)<0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "invalid VL location"); /* Get new dataset's property list object */ if (NULL == (new_plist = H5I_object(new_dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list"); /* Set the alloc_time for the dataset, in case the default was used */ if(H5P_set(new_plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, NULL, "can't set allocation time"); if(H5P_get(new_plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); if(H5P_get(new_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve external file list"); /* Total raw data size */ if(H5P_get(new_plist, H5D_CRT_LAYOUT_NAME, &(new_dset->layout.type)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve layout"); new_dset->layout.ndims = H5S_get_simple_extent_ndims(space) + 1; assert((unsigned)(new_dset->layout.ndims) <= NELMTS(new_dset->layout.dim)); new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(new_dset->type); new_dset->layout.addr = HADDR_UNDEF; /* Initialize to no address */ switch (new_dset->layout.type) { case H5D_CONTIGUOUS: /* * 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. */ if ((ndims=H5S_get_simple_extent_dims(space, new_dset->layout.dim, max_dim))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize contiguous storage"); for (i=1; inew_dset->layout.dim[i]) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible"); } if (efl.nused>0) { hsize_t max_points = H5S_get_npoints_max (space); hsize_t max_storage = H5O_efl_total_size (&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"); } } else if (ndims>0 && max_dim[0]>new_dset->layout.dim[0]) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset"); } break; case H5D_CHUNKED: /* * Chunked storage allows any type of data space extension, so we * don't even bother checking. */ if(chunk_ndims != H5S_get_simple_extent_ndims(space)) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space"); if (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(new_plist, H5D_CRT_CHUNK_SIZE_NAME, chunk_size) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve chunk size"); if (H5S_get_simple_extent_dims(space, NULL, max_dim)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions"); for (u=0; ulayout.ndims-1; u++) { if(max_dim[u] != H5S_UNLIMITED && max_dim[u] < chunk_size[u]) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions"); } /* Set the dataset's chunk sizes from the property list's chunk sizes */ for (u=0; ulayout.ndims-1; u++) new_dset->layout.dim[u] = chunk_size[u]; break; case H5D_COMPACT: /* * Compact dataset is stored in dataset object header message of * layout. */ new_dset->layout.size = H5S_get_simple_extent_npoints(space) * H5T_get_size(type); /* Verify data size is smaller than maximum header message size * (64KB) minus other layout message fields. */ comp_data_size=H5O_MAX_SIZE-H5O_layout_meta_size(f, &(new_dset->layout)); if(new_dset->layout.size > comp_data_size) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "compact dataset size is bigger than header message maximum size"); if ((ndims=H5S_get_simple_extent_dims(space, new_dset->layout.dim, max_dim))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize dimension size of compact dataset storage"); /* remember to check if size is small enough to fit header message */ break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* end switch */ /* Create (open for write access) an object header */ if (H5O_create(f, 256, &(new_dset->ent)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to create dataset object header"); /* Retrieve properties of fill value and others. Copy them into new fill * value struct. Convert the fill value to the dataset type and write * the message */ if(H5P_get(new_plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); if(H5P_get(new_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill time"); if(H5P_fill_value_defined(new_plist, &fill_status)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't tell if fill value defined"); if(fill_status== H5D_FILL_VALUE_DEFAULT || fill_status==H5D_FILL_VALUE_USER_DEFINED) { if(H5P_get(new_plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve fill value"); if(NULL==H5O_copy(H5O_FILL, &fill_prop, &fill)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,NULL, "unable to copy fill value"); if (fill_prop.buf && fill_prop.size>0 && H5O_fill_convert(&fill, new_dset->type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to convert fill value to dataset type"); fill.fill_defined = TRUE; } else if(fill_status==H5D_FILL_VALUE_UNDEFINED) { fill.size = -1; fill.type = fill.buf = NULL; fill.fill_defined = FALSE; } else { HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, NULL, "unable to determine if fill value is defined"); } /* end else */ fill.alloc_time = alloc_time; fill.fill_time = fill_time; if(fill.fill_defined == FALSE && fill_time != H5D_FILL_TIME_NEVER) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,NULL, "unable to create dataset"); /* Write new fill value message */ if (H5O_modify(&(new_dset->ent), H5O_FILL_NEW, 0, H5O_FLAG_CONSTANT, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to update fill value header message"); H5O_reset(H5O_FILL, &fill_prop); if(fill.buf && (NULL==H5O_copy(H5O_FILL, &fill, &fill_prop))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT,NULL,"unable to copy fill value"); H5O_reset(H5O_FILL_NEW, &fill); /* Write old fill value */ if (fill_prop.buf && H5O_modify(&(new_dset->ent), H5O_FILL, 0, H5O_FLAG_CONSTANT, &fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to update fill value header message"); if(H5P_set(new_plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, NULL, "can't set fill value"); /* Update the type and space header messages */ if (H5O_modify(&(new_dset->ent), H5O_DTYPE, 0, H5O_FLAG_CONSTANT|H5O_FLAG_SHARED, new_dset->type)<0 || H5S_modify(&(new_dset->ent), space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to update type or space header messages"); /* Update the filters message */ if(H5P_get(new_plist, H5D_CRT_DATA_PIPELINE_NAME, &dcpl_pline) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "Can't retrieve pipeline filter"); if (dcpl_pline.nfilters>0 && H5O_modify (&(new_dset->ent), H5O_PLINE, 0, H5O_FLAG_CONSTANT, &dcpl_pline) < 0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update filter header message"); /* * Add a modification time message. */ if (H5O_touch(&(new_dset->ent), TRUE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to update modification time message"); /* Give the dataset a name */ if (H5G_insert(loc, name, &(new_dset->ent)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset"); /* * Allocate storage if space allocate time is early; otherwise delay allocation until later. */ if(alloc_time==H5D_ALLOC_TIME_EARLY) if (H5D_alloc_storage(f, new_dset,H5D_ALLOC_CREATE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); /* Update external storage message */ if (efl.nused>0) { size_t heap_size = H5HL_ALIGN (1); for (i=0; ient), H5O_EFL, 0, H5O_FLAG_CONSTANT, &efl)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update external file list message"); } /* end if */ /* Update layout message */ if (H5D_COMPACT != new_dset->layout.type && H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, 0, &(new_dset->layout))<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update layout"); /* Success */ ret_value = new_dset; done: if (!ret_value && new_dset) { if (new_dset->type) H5T_close(new_dset->type); if (H5F_addr_defined(new_dset->ent.header)) H5O_close(&(new_dset->ent)); new_dset->ent.file = NULL; H5FL_FREE(H5D_t,new_dset); } FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_isa * * Purpose: Determines if an object has the requisite messages for being * a dataset. * * Return: Success: TRUE if the required dataset messages are * present; FALSE otherwise. * * Failure: FAIL if the existence of certain messages * cannot be determined. * * Programmer: Robb Matzke * Monday, November 2, 1998 * * Modifications: * *------------------------------------------------------------------------- */ htri_t H5D_isa(H5G_entry_t *ent) { htri_t exists; htri_t ret_value=TRUE; /* Return value */ FUNC_ENTER_NOAPI(H5D_isa, FAIL); assert(ent); /* Data type */ if ((exists=H5O_exists(ent, H5O_DTYPE, 0))<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read object header"); } else if (!exists) { HGOTO_DONE(FALSE); } /* Layout */ if ((exists=H5O_exists(ent, H5O_LAYOUT, 0))<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read object header"); } else if (!exists) { HGOTO_DONE(FALSE); } done: FUNC_LEAVE(ret_value); } /* *------------------------------------------------------------------------- * Function: H5D_open * * Purpose: Finds a dataset named NAME in file F and builds a descriptor * for it, opening it for access. * * Return: Success: Pointer to a new dataset descriptor. * * Failure: NULL * * Errors: * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space message is no longer cached in the dataset struct. * * Quincey Koziol, 12 Oct 1998 * Moved guts of function into H5D_open_oid * * Pedro Vicente, 18 Sep 2002 * Added `id to name' support. * *------------------------------------------------------------------------- */ H5D_t * H5D_open(H5G_entry_t *loc, const char *name) { H5D_t *dataset = NULL; /*the dataset which was found */ H5D_t *ret_value = NULL; /*return value */ H5G_entry_t ent; /*dataset symbol table entry */ FUNC_ENTER_NOAPI(H5D_open, NULL); /* check args */ assert (loc); assert (name && *name); /* Find the dataset object */ if (H5G_find(loc, name, NULL, &ent) < 0) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found"); /* Open the dataset object */ if ((dataset=H5D_open_oid(&ent)) ==NULL) HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found"); /* Success */ ret_value = dataset; done: /*Free the ID to name buffer */ H5G_free_ent_name(&ent); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_open_oid * * Purpose: Opens a dataset for access. * * Return: Dataset pointer on success, NULL on failure * * Errors: * * Programmer: Quincey Koziol * Monday, October 12, 1998 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to set property for generic property list. * * Raymond Lu * Feb 26, 2002 * A new fill value message and two new properties are added. * * Pedro Vicente, 22 Aug 2002 * Added a deep copy of the symbol table entry * *------------------------------------------------------------------------- */ H5D_t * H5D_open_oid(H5G_entry_t *ent) { H5D_t *dataset = NULL; /*new dataset struct */ H5D_t *ret_value = NULL; /*return value */ H5O_fill_new_t fill = {NULL, 0, NULL, H5D_ALLOC_TIME_LATE, H5D_FILL_TIME_ALLOC, TRUE}; H5O_fill_t fill_prop = {NULL, 0, NULL}; H5O_pline_t pline; /* I/O pipeline information */ H5O_efl_t efl; /* External file information */ H5D_layout_t layout; /* Dataset layout */ int chunk_ndims; H5P_genplist_t *plist; /* Property list */ FUNC_ENTER_NOAPI(H5D_open_oid, NULL); /* check args */ assert (ent); /* Allocate the dataset structure */ if(NULL==(dataset = H5D_new(H5P_DEFAULT))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); /* Deep copy of the symbol table entry */ if (H5G_ent_copy(ent,&(dataset->ent))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to copy entry"); /* Find the dataset object */ if (H5O_open(&(dataset->ent)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open"); /* Get the type and space */ if (NULL==(dataset->type=H5O_read(&(dataset->ent), H5O_DTYPE, 0, NULL))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load type info from dataset header"); /* Get dataset creation property list object */ if (NULL == (plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "can't get dataset creation property list"); /* Get the optional filters message */ HDmemset(&pline,0,sizeof(H5O_pline_t)); if(NULL == H5O_read(&(dataset->ent), H5O_PLINE, 0, &pline)) { H5E_clear(); HDmemset(&pline, 0, sizeof(pline)); } if(H5P_set(plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set pipeline"); /* If MPIO or MPIPOSIX is used, no filter support yet. */ if((IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file)) && pline.nfilters > 0) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel IO does not support filters yet"); /* * 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_read(&(dataset->ent), H5O_LAYOUT, 0, &(dataset->layout))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to read data layout message"); switch (dataset->layout.type) { case H5D_CONTIGUOUS: layout = H5D_CONTIGUOUS; if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout"); 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 data type. */ layout = H5D_CHUNKED; chunk_ndims = dataset->layout.ndims - 1; if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout"); if(H5P_set(plist, H5D_CRT_CHUNK_DIM_NAME, &chunk_ndims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set chunk dimensions"); if(H5P_set(plist, H5D_CRT_CHUNK_SIZE_NAME, dataset->layout.dim) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set chunk size"); break; case H5D_COMPACT: layout = H5D_COMPACT; if(H5P_set(plist, H5D_CRT_LAYOUT_NAME, &layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set layout"); break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* end switch */ /* Retrieve & release the previous fill-value settings */ if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't get fill value"); H5O_reset(H5O_FILL, &fill_prop); /* Get the new fill value message */ if(NULL == H5O_read(&(dataset->ent), H5O_FILL_NEW, 0, &fill)) { H5E_clear(); HDmemset(&fill, 0, sizeof(fill)); /* Set the space allocation time appropriately, based on the type of dataset storage */ switch (dataset->layout.type) { case H5D_COMPACT: fill.alloc_time=H5D_ALLOC_TIME_EARLY; break; case H5D_CONTIGUOUS: fill.alloc_time=H5D_ALLOC_TIME_LATE; break; case H5D_CHUNKED: fill.alloc_time=H5D_ALLOC_TIME_INCR; break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* end switch */ } /* end if */ if(fill.fill_defined) { if(NULL==H5O_copy(H5O_FILL, &fill, &fill_prop)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "can't copy fill value"); } else { /* For compatibility with v1.4. Retrieve the old fill value message. * If size is 0, make it -1 for undefined. */ if(NULL == H5O_read(&(dataset->ent), H5O_FILL, 0, &fill_prop)) { H5E_clear(); HDmemset(&fill_prop, 0, sizeof(fill_prop)); } if(fill_prop.size == 0) { fill_prop.type = fill_prop.buf = NULL; fill_prop.size = (size_t)-1; } } /* end else */ /* Set fill value properties */ if(H5P_set(plist, H5D_CRT_FILL_VALUE_NAME, &fill_prop) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); if(H5P_set(plist, H5D_CRT_ALLOC_TIME_NAME, &fill.alloc_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); if(H5P_set(plist, H5D_CRT_FILL_TIME_NAME, &fill.fill_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set fill value"); /* Get the external file list message, which might not exist. Space is * also undefined when space allocate time is H5D_ALLOC_TIME_LATE. */ if( !H5F_addr_defined(dataset->layout.addr)) { HDmemset(&efl,0,sizeof(H5O_efl_t)); if(NULL != H5O_read(&(dataset->ent), H5O_EFL, 0, &efl)) if(H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, NULL, "can't set external file list"); } /* * 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->ent.file) & H5F_ACC_RDWR) && (dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) && (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file))) { if (H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_OPEN)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize file storage"); } /* Success */ ret_value = dataset; done: if (ret_value==NULL && dataset) { if (H5F_addr_defined(dataset->ent.header)) H5O_close(&(dataset->ent)); if (dataset->type) H5T_close(dataset->type); dataset->ent.file = NULL; H5FL_FREE(H5D_t,dataset); } FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * 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 * * Errors: * DATASET CANTINIT Couldn't free the type or space, * but the dataset was freed anyway. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space message is no longer cached in the dataset struct. * *------------------------------------------------------------------------- */ herr_t H5D_close(H5D_t *dataset) { unsigned free_failed; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_close, FAIL); /* check args */ assert(dataset && dataset->ent.file); /* * Release data type and creation property list -- there isn't much we * can do if one of these fails, so we just continue. */ free_failed = (H5T_close(dataset->type) < 0 || H5I_dec_ref(dataset->dcpl_id) < 0); /* Update header message of layout for compact dataset. */ if(dataset->layout.type==H5D_COMPACT && dataset->layout.dirty) { if(H5O_modify(&(dataset->ent), H5O_LAYOUT, 0, 0, &(dataset->layout))<0) HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message"); dataset->layout.dirty = FALSE; } /* end if */ /* Close the dataset object */ H5O_close(&(dataset->ent)); /* * 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 assert() * above). */ dataset->ent.file = NULL; /* Free the buffer for the raw data for compact datasets */ if(dataset->layout.type==H5D_COMPACT) dataset->layout.buf=H5MM_xfree(dataset->layout.buf); H5FL_FREE(H5D_t,dataset); if (free_failed) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free the type or creation property list, but the dataset was freed anyway."); done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_read * * Purpose: Reads (part of) a DATASET into application memory BUF. See * H5Dread() for complete details. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 1998-06-09 * The data space is no longer cached in the dataset struct. * * Robb Matzke, 1998-08-11 * Added timing calls around all the data space I/O functions. * * rky, 1998-09-18 * Added must_convert to do non-optimized read when necessary. * * Quincey Koziol, 1999-07-02 * Changed xfer_parms parameter to xfer plist parameter, so it * could be passed to H5T_convert. * * Albert Cheng, 2000-11-21 * Added the code that when it detects it is not safe to process a * COLLECTIVE read request without hanging, it changes it to * INDEPENDENT calls. * * Albert Cheng, 2000-11-27 * Changed to use the optimized MPIO transfer for Collective calls only. * * Raymond Lu, 2001-10-2 * Changed the way to retrieve property for generic property list. * * Raymond Lu, 2002-2-26 * For the new fill value design, data space can either be allocated * or not allocated at this stage. Fill value or data from space is * returned to outgoing buffer. * * QAK - 2002/04/02 * Removed the must_convert parameter and move preconditions to * H5S__opt_possible() routine * *------------------------------------------------------------------------- */ herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/) { hsize_t nelmts; /*total number of elmts */ hsize_t smine_start; /*strip mine start loc */ hsize_t n, smine_nelmts; /*elements per strip */ uint8_t *tconv_buf = NULL; /*data type conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ H5T_path_t *tpath = NULL; /*type conversion info */ hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ H5S_conv_t *sconv=NULL; /*space conversion funcs*/ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ H5S_sel_iter_t bkg_iter; /*background iteration info*/ H5S_sel_iter_t file_iter; /*file selection iteration info*/ herr_t ret_value = SUCCEED; /*return value */ herr_t status; /*function return status*/ size_t src_type_size; /*size of source type */ size_t dst_type_size; /*size of destination type*/ size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ H5T_bkg_t need_bkg; /*type of background buf*/ H5S_t *free_this_space=NULL; /*data space to free */ #ifdef H5_HAVE_PARALLEL H5FD_mpio_dxpl_t *dx = NULL; H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ hbool_t xfer_mode_changed=0; /*xfer_mode needs restore */ hbool_t doing_mpio=0; /*This is an MPIO access */ #endif /*H5_HAVE_PARALLEL*/ #ifdef H5S_DEBUG H5_timer_t timer; #endif H5O_efl_t efl; /* External File List info */ H5O_fill_t fill; /* Fill value info */ H5D_fill_time_t fill_time; /* When to write the fill values */ H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */ H5P_genplist_t *dc_plist; /* Dataset creation roperty list */ unsigned sconv_flags=0; /* Flags for the space conversion */ FUNC_ENTER_NOAPI(H5D_read, FAIL); /* check args */ assert(dataset && dataset->ent.file); assert(mem_type); assert(buf); /* Initialize these before any errors can occur */ HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t)); HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t)); HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t)); /* Get the dataset's creation property list */ if (NULL == (dc_plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the dataset transfer property list */ if (NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if (!file_space) { if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header"); file_space = free_this_space; } /* end if */ if (!mem_space) mem_space = file_space; nelmts = (*mem_space->select.get_npoints)(mem_space); #ifdef H5_HAVE_PARALLEL /* Collect Parallel I/O information for possible later use */ if (H5FD_MPIO==H5P_peek_hid_t(dx_plist,H5D_XFER_VFL_ID_NAME)) { doing_mpio++; if (NULL == (dx=H5P_peek_voidp(dx_plist,H5D_XFER_VFL_INFO_NAME))) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to retrieve data xfer info"); } else { xfer_mode = dx->xfer_mode; } } /* end if */ /* Collective access is not permissible without the MPIO or MPIPOSIX driver */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && !(IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPIO & MPIPOSIX drivers only"); /* Set the "parallel I/O possible" flag, for H5S_find() */ if (H5S_mpi_opt_types_g && IS_H5FD_MPIO(dataset->ent.file)) { /* Only collective write should call this since it eventually * calls MPI_File_set_view which is a collective call. * See H5S_mpio_spaces_xfer() for details. */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE; } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Make certain that the number of elements in each selection is the same */ if (nelmts!=(*file_space->select.get_npoints) (file_space)) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); /* Retrieve dataset properties */ if(H5P_fill_value_defined(dc_plist, &fill_status)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined"); if((fill_status==H5D_FILL_VALUE_DEFAULT || fill_status==H5D_FILL_VALUE_USER_DEFINED) && H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill value"); if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill time"); if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); /* If space hasn't been allocated and not using external storage, * return fill value to buffer if fill time is upon allocation, or * do nothing if fill time is never. If the dataset is compact and * fill time is NEVER, there is no way to tell whether part of data * has been overwritten. So just proceed in reading. */ if(nelmts > 0 && efl.nused==0 && dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) { /* Should be impossible, but check anyway... */ if(fill_status == H5D_FILL_VALUE_UNDEFINED && fill_time == H5D_FILL_TIME_ALLOC) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "read failed: dataset doesn't exist, no data can be read"); /* If we're never going to fill this dataset, just leave the junk in the user's buffer */ if(fill_time == H5D_FILL_TIME_NEVER) HGOTO_DONE(SUCCEED); /* Go fill the user's selection with the dataset's fill value */ if(H5D_fill(fill.buf,fill.type,buf,mem_type,mem_space)<0) { HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed"); } else HGOTO_DONE(SUCCEED); } /* end if */ /* * Locate the type conversion function and data space conversion * functions, and set up the element numbering information. If a data * type conversion is necessary then register data type atoms. Data type * conversion is necessary if the user has set the `need_bkg' to a high * enough value in xfer_parms since turning off data type conversion also * turns off background preservation. */ if (NULL==(tpath=H5T_path_find(dataset->type, mem_type, NULL, NULL))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } else if (!H5T_IS_NOOP(tpath)) { if ((src_id=H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0 || (dst_id=H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); } /* end if */ /* Set the storage flags for the space conversion check */ switch(dataset->layout.type) { case H5D_COMPACT: sconv_flags |= H5S_CONV_STORAGE_COMPACT; break; case H5D_CONTIGUOUS: sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS; break; case H5D_CHUNKED: sconv_flags |= H5S_CONV_STORAGE_CHUNKED; break; default: assert(0 && "Unhandled layout type!"); } /* end switch */ /* Get dataspace functions */ if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space"); /* * If there is no type conversion then read directly into the * application's buffer. This saves at least one mem-to-mem copy. */ if (H5T_IS_NOOP(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ assert(dataset->layout.addr!=HADDR_UNDEF || efl.nused>0 || dataset->layout.type==H5D_COMPACT); status = (sconv->read)(dataset->ent.file, &(dataset->layout), dc_plist, H5T_get_size(dataset->type), file_space, mem_space, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].read_timer), &timer); sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type); sconv->stats[1].read_ncalls++; #endif /* Check return value from optimized read */ if (status<0) { HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed"); } else /* direct xfer accomplished successfully */ HGOTO_DONE(SUCCEED); } /* end if */ #ifdef H5_HAVE_PARALLEL /* The following may not handle a collective call correctly * since it does not ensure all processes can handle the read * request according to the MPI collective specification. * Do the collective request via independent mode. */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) { /* Kludge: change the xfer_mode to independent, handle the request, * then xfer_mode before return. * Better way is to get a temporary data_xfer property with * INDEPENDENT xfer_mode and pass it downwards. */ dx->xfer_mode = H5FD_MPIO_INDEPENDENT; xfer_mode_changed++; /* restore it before return */ #ifdef H5D_DEBUG if (H5DEBUG(D)) { fprintf(H5DEBUG(D), "H5D: Cannot handle this COLLECTIVE read request. Do it via INDEPENDENT calls\n" "dx->xfermode was %d, changed to %d\n", xfer_mode, dx->xfer_mode); } /* end if */ #endif } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* * This is the general case. */ /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(dataset->type); dst_type_size = H5T_get_size(mem_type); target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); request_nelmts = target_size / MAX(src_type_size, dst_type_size); /* Figure out the strip mine size. */ if ((*file_space->select.iter_init)(file_space, src_type_size, &file_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); if ((*mem_space->select.iter_init)(mem_space, dst_type_size, &mem_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); if ((*mem_space->select.iter_init)(mem_space, dst_type_size, &bkg_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); /* Sanity check elements in temporary buffer */ if (request_nelmts<=0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); /* * Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a * buffer which is the exact size, we allocate the target size. The * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ if (tpath->cdata.need_bkg) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); need_bkg = MAX(tpath->cdata.need_bkg, need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { /* Allocate temporary buffer */ if((tconv_buf=H5FL_BLK_ALLOC(type_conv,target_size,0))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } /* end if */ if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); if((bkg_buf=H5FL_BLK_ALLOC(type_conv,(size_t)(request_nelmts*dst_type_size),0))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ /* Start strip mining... */ for (smine_start=0; smine_startselect.iter_nelmts)(&file_iter)==(nelmts-smine_start)); smine_nelmts = MIN(request_nelmts, (nelmts-smine_start)); /* * Gather the data from disk into the data type conversion * buffer. Also gather data from application to background buffer * if necessary. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif /* Sanity check that space is allocated, then read data from it */ assert(dataset->layout.addr!=HADDR_UNDEF || efl.nused > 0); n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), dc_plist, src_type_size, file_space, &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].gath_timer), &timer); sconv->stats[1].gath_nbytes += n * src_type_size; sconv->stats[1].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); if (need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5S_select_mgath(buf, dst_type_size, mem_space, &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].bkg_timer), &timer); sconv->stats[1].bkg_nbytes += n * dst_type_size; sconv->stats[1].bkg_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); } /* end if */ /* * Perform data type conversion. */ if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); /* * Scatter the data into memory. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5S_select_mscat(tconv_buf, dst_type_size, mem_space, &mem_iter, smine_nelmts, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].scat_timer), &timer); sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size; sconv->stats[1].scat_ncalls++; #endif if (status<0) HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed"); } /* end for */ done: #ifdef H5_HAVE_PARALLEL /* restore xfer_mode due to the kludge */ if (doing_mpio && xfer_mode_changed) { #ifdef H5D_DEBUG if (H5DEBUG(D)) { fprintf (H5DEBUG(D), "H5D: dx->xfermode was %d, restored to %d\n", dx->xfer_mode, xfer_mode); } /* end if */ #endif dx->xfer_mode = xfer_mode; } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Release selection iterators */ (*file_space->select.iter_release)(&file_iter); (*mem_space->select.iter_release)(&mem_iter); (*mem_space->select.iter_release)(&bkg_iter); if (src_id >= 0) H5I_dec_ref(src_id); if (dst_id >= 0) H5I_dec_ref(dst_id); assert(dx_plist); if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(type_conv,bkg_buf); if (free_this_space) H5S_close(free_this_space); FUNC_LEAVE(ret_value); } /* end H5D_read() */ /*------------------------------------------------------------------------- * Function: H5D_write * * Purpose: Writes (part of) a DATASET to a file from application memory * BUF. See H5Dwrite() for complete details. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space is no longer cached in the dataset struct. * * rky 980918 * Added must_convert to do non-optimized read when necessary. * * Quincey Koziol, 2 July 1999 * Changed xfer_parms parameter to xfer plist parameter, so it could * be passed to H5T_convert * * Albert Cheng, 2000-11-21 * Added the code that when it detects it is not safe to process a * COLLECTIVE write request without hanging, it changes it to * INDEPENDENT calls. * * Albert Cheng, 2000-11-27 * Changed to use the optimized MPIO transfer for Collective calls only. * * Raymond Lu, 2001-10-2 * Changed the way to retrieve property for generic property list. * * Raymond Lu, 2002-2-26 * For the new fill value design, space may not be allocated until * this function is called. Allocate and initialize space if it * hasn't been. * * QAK - 2002/04/02 * Removed the must_convert parameter and move preconditions to * H5S__opt_possible() routine * *------------------------------------------------------------------------- */ herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, hid_t dxpl_id, const void *buf) { hsize_t nelmts; /*total number of elmts */ hsize_t smine_start; /*strip mine start loc */ hsize_t n, smine_nelmts; /*elements per strip */ uint8_t *tconv_buf = NULL; /*data type conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ H5T_path_t *tpath = NULL; /*type conversion info */ hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ H5S_conv_t *sconv=NULL; /*space conversion funcs*/ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ H5S_sel_iter_t bkg_iter; /*background iteration info*/ H5S_sel_iter_t file_iter; /*file selection iteration info*/ herr_t ret_value = SUCCEED; /*return value */ herr_t status; /*function return status*/ size_t src_type_size; /*size of source type */ size_t dst_type_size; /*size of destination type*/ size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ H5T_bkg_t need_bkg; /*type of background buf*/ H5S_t *free_this_space=NULL; /*data space to free */ #ifdef H5_HAVE_PARALLEL H5FD_mpio_dxpl_t *dx = NULL; H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ hbool_t xfer_mode_changed=0; /*xfer_mode needs restore */ hbool_t doing_mpio=0; /*This is an MPIO access */ #endif /*H5_HAVE_PARALLEL*/ #ifdef H5S_DEBUG H5_timer_t timer; #endif H5O_efl_t efl; /* External File List info */ H5O_fill_t fill; /* Fill value info */ H5D_fill_time_t fill_time; /* When to write the fill values */ H5D_alloc_time_t alloc_time; /* When to allocate raw data space */ H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */ H5P_genplist_t *dc_plist; /* Dataset creation roperty list */ unsigned sconv_flags=0; /* Flags for the space conversion */ FUNC_ENTER_NOAPI(H5D_write, FAIL); /* check args */ assert(dataset && dataset->ent.file); assert(mem_type); assert(buf); /* Initialize these before any errors can occur */ HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t)); HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t)); HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t)); /* Get the dataset's creation property list */ if (NULL == (dc_plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the dataset transfer property list */ if (NULL == (dx_plist = H5P_object_verify(dxpl_id,H5P_DATASET_XFER))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if (!file_space) { if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header"); file_space = free_this_space; } /* end if */ if (!mem_space) mem_space = file_space; nelmts = (*mem_space->select.get_npoints)(mem_space); /* If MPIO or MPIPOSIX is used, no VL datatype support yet. */ /* This is because they use the global heap in the file and we don't */ /* support parallel access of that yet */ if ( (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file)) && H5T_get_class(mem_type)==H5T_VLEN) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet"); /* If MPIO or MPIPOSIX is used, no dataset region reference datatype support yet. */ /* This is because they use the global heap in the file and we don't */ /* support parallel access of that yet */ if ((IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file)) && H5T_get_class(mem_type)==H5T_REFERENCE && H5T_get_ref_type(mem_type)==H5R_DATASET_REGION) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet"); if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR)) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file"); #ifdef H5_HAVE_PARALLEL /* Collect Parallel I/O information for possible later use */ if (H5FD_MPIO==H5P_peek_hid_t(dx_plist,H5D_XFER_VFL_ID_NAME)) { doing_mpio++; if (NULL==(dx=H5P_peek_voidp(dx_plist,H5D_XFER_VFL_INFO_NAME))) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to retrieve data xfer info"); } else { xfer_mode = dx->xfer_mode; } } /* end if */ /* Collective access is not permissible without the MPIO or MPIPOSIX driver */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && !(IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPIO driver only"); /* If dataset is compact, collective access is only allowed when file space * selection is H5S_ALL */ if(doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && dataset->layout.type==H5D_COMPACT) { if(file_space->select.type != H5S_SEL_ALL) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access to compact dataset doesn't support partial access"); } /* Set the "parallel I/O possible" flag, for H5S_find() */ if (H5S_mpi_opt_types_g && IS_H5FD_MPIO(dataset->ent.file)) { /* Only collective write should call this since it eventually * calls MPI_File_set_view which is a collective call. * See H5S_mpio_spaces_xfer() for details. */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE; } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Make certain that the number of elements in each selection is the same */ if (nelmts!=(*file_space->select.get_npoints) (file_space)) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); /* Retrieve dataset properties */ if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill value"); if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill time"); if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); if(H5P_get(dc_plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); /* Allocate data space and initialize it if it hasn't been. */ if(nelmts > 0 && dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) { /* Allocate storage */ if(H5D_alloc_storage(dataset->ent.file, dataset,H5D_ALLOC_WRITE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage"); } /* end if */ /* * Locate the type conversion function and data space conversion * functions, and set up the element numbering information. If a data * type conversion is necessary then register data type atoms. Data type * conversion is necessary if the user has set the `need_bkg' to a high * enough value in xfer_parms since turning off data type conversion also * turns off background preservation. */ if (NULL==(tpath=H5T_path_find(mem_type, dataset->type, NULL, NULL))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } else if (!H5T_IS_NOOP(tpath)) { if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0 || (dst_id = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); } /* end if */ /* Set the storage flags for the space conversion check */ switch(dataset->layout.type) { case H5D_COMPACT: sconv_flags |= H5S_CONV_STORAGE_COMPACT; break; case H5D_CONTIGUOUS: sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS; break; case H5D_CHUNKED: sconv_flags |= H5S_CONV_STORAGE_CHUNKED; break; default: assert(0 && "Unhandled layout type!"); } /* end switch */ /* Get dataspace functions */ if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space"); /* * If there is no type conversion then write directly from the * application's buffer. This saves at least one mem-to-mem copy. */ if (H5T_IS_NOOP(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = (sconv->write)(dataset->ent.file, &(dataset->layout), dc_plist, H5T_get_size(dataset->type), file_space, mem_space, dxpl_id, buf); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].write_timer), &timer); sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type); sconv->stats[0].write_ncalls++; #endif /* Check return value from optimized write */ if (status<0) { HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed"); } else /* direct xfer accomplished successfully */ HGOTO_DONE(SUCCEED); } /* end if */ #ifdef H5_HAVE_PARALLEL /* The following may not handle a collective call correctly * since it does not ensure all processes can handle the write * request according to the MPI collective specification. * Do the collective request via independent mode. */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) { /* Kludge: change the xfer_mode to independent, handle the request, * then xfer_mode before return. * Better way is to get a temporary data_xfer property with * INDEPENDENT xfer_mode and pass it downwards. */ dx->xfer_mode = H5FD_MPIO_INDEPENDENT; xfer_mode_changed++; /* restore it before return */ #ifdef H5D_DEBUG if (H5DEBUG(D)) { fprintf(H5DEBUG(D), "H5D: Cannot handle this COLLECTIVE write request. Do it via INDEPENDENT calls\n" "dx->xfermode was %d, changed to %d\n", xfer_mode, dx->xfer_mode); } /* end if */ #endif } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* * This is the general case. */ /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(mem_type); dst_type_size = H5T_get_size(dataset->type); target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); request_nelmts = target_size / MAX (src_type_size, dst_type_size); /* Sanity check elements in temporary buffer */ if (request_nelmts<=0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); /* Figure out the strip mine size. */ if ((*file_space->select.iter_init)(file_space, dst_type_size, &file_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); if ((*mem_space->select.iter_init)(mem_space, src_type_size, &mem_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); if ((*file_space->select.iter_init)(file_space, dst_type_size, &bkg_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); /* * Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a * buffer which is the exact size, we allocate the target size. The * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ if (tpath->cdata.need_bkg) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); need_bkg = MAX (tpath->cdata.need_bkg, need_bkg); } else if(H5T_detect_class(dataset->type, H5T_VLEN)) { /* Old data is retrieved into background buffer for VL datatype. The * data is used later for freeing heap objects. */ need_bkg = H5T_BKG_YES; } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { /* Allocate temporary buffer */ if((tconv_buf=H5FL_BLK_ALLOC(type_conv,target_size,0))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } /* end if */ if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); if((bkg_buf=H5FL_BLK_ALLOC(type_conv,(size_t)(request_nelmts*dst_type_size),1))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ /* Start strip mining... */ for (smine_start=0; smine_startselect.iter_nelmts)(&file_iter)==(nelmts-smine_start)); smine_nelmts = MIN(request_nelmts, (nelmts-smine_start)); /* * Gather data from application buffer into the data type conversion * buffer. Also gather data from the file into the background buffer * if necessary. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5S_select_mgath(buf, src_type_size, mem_space, &mem_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].gath_timer), &timer); sconv->stats[0].gath_nbytes += n * src_type_size; sconv->stats[0].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed"); if (need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), dc_plist, dst_type_size, file_space, &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].bkg_timer), &timer); sconv->stats[0].bkg_nbytes += n * dst_type_size; sconv->stats[0].bkg_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed"); } /* end if */ /* * Perform data type conversion. */ if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); /* * Scatter the data out to the file. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), dc_plist, dst_type_size, file_space, &file_iter, smine_nelmts, dxpl_id, tconv_buf); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].scat_timer), &timer); sconv->stats[0].scat_nbytes += smine_nelmts * dst_type_size; sconv->stats[0].scat_ncalls++; #endif if (status<0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed"); } /* end for */ /* * Update modification time. We have to do this explicitly because * writing to a dataset doesn't necessarily change the object header. */ if (H5O_touch(&(dataset->ent), FALSE)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time"); done: #ifdef H5_HAVE_PARALLEL /* restore xfer_mode due to the kludge */ if (doing_mpio && xfer_mode_changed) { #ifdef H5D_DEBUG if (H5DEBUG(D)) { fprintf (H5DEBUG(D), "H5D: dx->xfermode was %d, restored to %d\n", dx->xfer_mode, xfer_mode); } /* end if */ #endif dx->xfer_mode = xfer_mode; } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Release selection iterators */ (*file_space->select.iter_release)(&file_iter); (*mem_space->select.iter_release)(&mem_iter); (*file_space->select.iter_release)(&bkg_iter); if (src_id >= 0) H5I_dec_ref(src_id); if (dst_id >= 0) H5I_dec_ref(dst_id); assert(dx_plist); if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(type_conv,bkg_buf); if (free_this_space) H5S_close(free_this_space); FUNC_LEAVE(ret_value); } /* end H5D_write() */ /*------------------------------------------------------------------------- * Function: H5D_extend * * Purpose: Increases the size of a dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Friday, January 30, 1998 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to retrieve property for generic property * list. * *------------------------------------------------------------------------- */ herr_t H5D_extend (H5D_t *dataset, const hsize_t *size) { int changed; /* Flag to indicate that the dataspace was successfully extended */ H5S_t *space = NULL; /* Dataset's dataspace */ H5D_alloc_time_t alloc_time; /* When to allocate raw data space */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_extend, FAIL); /* Check args */ assert (dataset); assert (size); /* Get the dataset creation property list */ if (NULL == (plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if(H5P_get(plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); /* * NOTE: Restrictions on extensions were checked when the dataset was * created. All extensions are allowed here since none should be * able to muck things up. */ /* Increase the size of the data space */ if (NULL==(space=H5S_read (&(dataset->ent)))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space info from dataset header"); if ((changed=H5S_extend (space, size))<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to increase size of data space"); if (changed>0){ /* Save the new dataspace in the file if necessary */ if (H5S_modify (&(dataset->ent), space)<0) HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); /* Allocate space for the new parts of the dataset, if appropriate */ if(alloc_time==H5D_ALLOC_TIME_EARLY) if (H5D_alloc_storage(dataset->ent.file, dataset, H5D_ALLOC_EXTEND)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); } /* end if */ done: H5S_close(space); FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5D_entof * * Purpose: Returns a pointer to the entry for a dataset. * * Return: Success: Ptr to entry * * Failure: NULL * * Programmer: Robb Matzke * Friday, April 24, 1998 * * Modifications: * *------------------------------------------------------------------------- */ H5G_entry_t * H5D_entof (H5D_t *dataset) { /* Use FUNC_ENTER_NOINIT here to avoid performance issues */ FUNC_ENTER_NOINIT(H5D_entof); FUNC_LEAVE( dataset ? &(dataset->ent) : NULL); } /*------------------------------------------------------------------------- * Function: H5D_typeof * * Purpose: Returns a pointer to the dataset's data type. The data type * is not copied. * * Return: Success: Ptr to the dataset's data type, uncopied. * * Failure: NULL * * Programmer: Robb Matzke * Thursday, June 4, 1998 * * Modifications: * *------------------------------------------------------------------------- */ H5T_t * H5D_typeof (H5D_t *dset) { /* Use FUNC_ENTER_NOINIT here to avoid performance issues */ FUNC_ENTER_NOINIT(H5D_typeof); assert (dset); assert (dset->type); FUNC_LEAVE (dset->type); } /*------------------------------------------------------------------------- * 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 * * Modifications: * *------------------------------------------------------------------------- */ H5F_t * H5D_get_file (const H5D_t *dset) { /* Use FUNC_ENTER_NOINIT here to avoid performance issues */ FUNC_ENTER_NOINIT(H5D_get_file); assert (dset); assert (dset->ent.file); FUNC_LEAVE (dset->ent.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 * * Modifications: * Quincey Koziol * Thursday, August 22, 2002 * Moved here from H5F_arr_create and moved more logic into * this function from places where it was being called. * *------------------------------------------------------------------------- */ static herr_t H5D_alloc_storage (H5F_t *f, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc) { H5P_genplist_t *plist; /* Dataset's creation property list */ H5O_efl_t efl; /* External File List info */ H5D_fill_time_t fill_time; /* When to write fill values */ H5D_alloc_time_t alloc_time; /* When to allocate raw data space */ struct H5O_layout_t *layout; /* The dataset's layout information */ hsize_t nbytes; /* The number of bytes in the dataset */ unsigned space_allocated=0; /* Flag to indicate that space was allocated */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_alloc_storage); /* check args */ assert (f); assert (dset); /* Get external file list properties */ if (NULL == (plist = H5I_object(dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); /* 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(efl.nused==0) { /* Get properties needed */ if(H5P_get(plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve fill time"); if(H5P_get(plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); /* Get a pointer to the dataset's layout information */ layout=&(dset->layout); switch (layout->type) { case H5D_CONTIGUOUS: if(layout->addr==HADDR_UNDEF) { /* Reserve space in the file for the entire array */ for (u=0, nbytes=1; undims; u++) nbytes *= layout->dim[u]; assert (nbytes>0); if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, nbytes))) HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space"); /* Indicate that we allocated space */ space_allocated=1; } /* end if */ break; case H5D_CHUNKED: if(layout->addr==HADDR_UNDEF) { /* Create the root of the B-tree that describes chunked storage */ if (H5F_istore_create (f, layout/*out*/)<0) HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize chunked storage"); /* Indicate that we allocated space */ space_allocated=1; } /* end if */ break; case H5D_COMPACT: /* Check if space is already allocated */ if(layout->buf==NULL) { /* Reserve space in layout header message for the entire array. */ assert(layout->size>0); if (NULL==(layout->buf=H5MM_malloc(layout->size))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory for compact dataset"); layout->dirty = TRUE; /* Indicate that we allocated space */ space_allocated=1; } /* end if */ break; default: assert ("not implemented yet" && 0); HGOTO_ERROR (H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout"); } /* end switch */ /* If we are filling the dataset on allocation, do that now */ if(fill_time==H5D_FILL_TIME_ALLOC && !(alloc_time==H5D_ALLOC_TIME_INCR && time_alloc==H5D_ALLOC_WRITE)) { if(H5D_init_storage(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); } /* end if */ /* Also update header message for layout with new address * (this is only for forward compatibility). */ if(space_allocated && time_alloc!=H5D_ALLOC_CREATE) if (H5O_modify (&(dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT, &(dset->layout)) < 0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message"); } /* end if */ done: FUNC_LEAVE (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 * * Modifications: * * Raymond Lu * Tuesday, October 2, 2001 * Changed the way to retrieve property for generic property * list. * *------------------------------------------------------------------------- */ static herr_t H5D_init_storage(H5D_t *dset) { hssize_t snpoints; /* Number of points in space (for error checking) */ size_t npoints; /* Number of points in space */ H5S_t *space = NULL; /* Dataset's dataspace */ H5O_fill_t fill; /* Fill value information */ H5O_efl_t efl; /* External File List info */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_init_storage); assert(dset); /* Get fill value, external file list, and data pipeline properties */ if (NULL == (plist = H5I_object(dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value"); if(H5P_get(plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve external file list"); /* Get the dataset's dataspace */ if (NULL==(space=H5S_read (&(dset->ent)))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space from dataset header"); /* Get the number of elements in the dataset's dataspace */ snpoints = H5S_get_simple_extent_npoints(space); assert(snpoints>=0); H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); switch (dset->layout.type) { case H5D_COMPACT: /* If the fill value is defined, initialize the data buffer with it */ if(fill.buf) /* Initialize the cached data buffer with the fill value */ H5V_array_fill(dset->layout.buf, fill.buf, fill.size, npoints); else /* If the fill value is default, zero set data buf. */ HDmemset(dset->layout.buf, 0, dset->layout.size); break; case H5D_CONTIGUOUS: if (H5F_contig_fill(dset->ent.file, H5P_DATASET_XFER_DEFAULT, &(dset->layout), plist, space, H5T_get_size(dset->type))<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. */ { /* We only handle simple data spaces so far */ int ndims; hsize_t dim[H5O_LAYOUT_NDIMS]; if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get simple data space info"); dim[ndims] = dset->layout.dim[ndims]; if (H5F_istore_allocate(dset->ent.file, H5P_DATASET_XFER_DEFAULT, &(dset->layout), dim, plist)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset"); } /* end if */ break; } /* end switch */ done: if (space) H5S_close(space); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dget_storage_size * * Purpose: Returns the amount of storage that is required for the * dataset. For chunked datasets this is the number of allocated * chunks times the chunk size. * * Return: Success: The amount of storage space allocated for the * dataset, not counting meta data. The return * value may be zero if no data has been stored. * * Failure: Zero * * Programmer: Robb Matzke * Wednesday, April 21, 1999 * * Modifications: * *------------------------------------------------------------------------- */ hsize_t H5Dget_storage_size(hid_t dset_id) { H5D_t *dset=NULL; hsize_t ret_value; /* Return value */ FUNC_ENTER_API(H5Dget_storage_size, 0); H5TRACE1("h","i",dset_id); /* Check args */ if (NULL==(dset=H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset"); /* Set return value */ ret_value = H5D_get_storage_size(dset); done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * 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 * * Modifications: * *------------------------------------------------------------------------- */ hsize_t H5D_get_storage_size(H5D_t *dset) { unsigned u; /* Index variable */ hsize_t ret_value; FUNC_ENTER_NOAPI(H5D_get_storage_size, 0); switch(dset->layout.type) { case H5D_CHUNKED: if(dset->layout.addr == HADDR_UNDEF) ret_value=0; else ret_value = H5F_istore_allocated(dset->ent.file, dset->layout.ndims, dset->layout.addr); break; case H5D_CONTIGUOUS: /* Datasets which are not allocated yet are using no space on disk */ if(dset->layout.addr == HADDR_UNDEF) ret_value=0; else { for (u=0, ret_value=1; ulayout.ndims; u++) ret_value *= dset->layout.dim[u]; } /* end else */ break; case H5D_COMPACT: ret_value = dset->layout.size; break; default: HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset type"); } done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5Diterate * * Purpose: This routine iterates over all the elements selected in a memory * buffer. The callback function is called once for each element selected * in the dataspace. The selection in the dataspace is modified so * that any elements already iterated over are removed from the selection * if the iteration is interrupted (by the H5D_operator_t function * returning non-zero) in the "middle" of the iteration and may be * re-started by the user where it left off. * * NOTE: Until "subtracting" elements from a selection is implemented, * the selection is not modified. * * Parameters: * void *buf; IN/OUT: Pointer to the buffer in memory containing * the elements to iterate over. * hid_t type_id; IN: Datatype ID for the elements stored in BUF. * hid_t space_id; IN: Dataspace ID for BUF, also contains the * selection to iterate over. * H5D_operator_t op; IN: Function pointer to the routine to be * called for each element in BUF iterated over. * void *operator_data; IN/OUT: Pointer to any user-defined data * associated with the operation. * * Operation information: * H5D_operator_t is defined as: * typedef herr_t (*H5D_operator_t)(void *elem, hid_t type_id, * hsize_t ndim, hssize_t *point, void *operator_data); * * H5D_operator_t parameters: * void *elem; IN/OUT: Pointer to the element in memory containing * the current point. * hid_t type_id; IN: Datatype ID for the elements stored in ELEM. * hsize_t ndim; IN: Number of dimensions for POINT array * hssize_t *point; IN: Array containing the location of the element * within the original dataspace. * void *operator_data; IN/OUT: Pointer to any user-defined data * associated with the operation. * * The return values from an operator are: * Zero causes the iterator to continue, returning zero when all * elements have been processed. * Positive causes the iterator to immediately return that positive * value, indicating short-circuit success. The iterator can be * restarted at the next element. * Negative causes the iterator to immediately return that value, * indicating failure. The iterator can be restarted at the next * element. * * 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 * Friday, June 11, 1999 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Diterate(void *buf, hid_t type_id, hid_t space_id, H5D_operator_t op, void *operator_data) { H5S_t *space = NULL; herr_t ret_value; FUNC_ENTER_API(H5Diterate, FAIL); H5TRACE5("e","xiixx",buf,type_id,space_id,op,operator_data); /* Check args */ if (NULL==op) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid operator"); if (buf==NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer"); if (H5I_DATATYPE != H5I_get_type(type_id)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid datatype"); if (NULL == (space = H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace"); ret_value=H5S_select_iterate(buf,type_id,space,op,operator_data); done: FUNC_LEAVE(ret_value); } /* end H5Diterate() */ /*------------------------------------------------------------------------- * Function: H5Dvlen_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 * Thursday, June 10, 1999 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf) { herr_t ret_value; FUNC_ENTER_API(H5Dvlen_reclaim, FAIL); H5TRACE4("e","iiix",type_id,space_id,plist_id,buf); /* Check args */ if (H5I_DATATYPE!=H5I_get_type(type_id) || H5I_DATASPACE!=H5I_get_type(space_id) || buf==NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument"); /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == plist_id) plist_id= H5P_DATASET_XFER_DEFAULT; if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); /* Call H5Diterate with args, etc. */ ret_value=H5Diterate(buf,type_id,space_id,H5T_vlen_reclaim,&plist_id); done: FUNC_LEAVE(ret_value); } /* end H5Dvlen_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 * * Modifications: * *------------------------------------------------------------------------- */ void * H5D_vlen_get_buf_size_alloc(size_t size, void *info) { H5T_vlen_bufsize_t *vlen_bufsize=(H5T_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(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 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_vlen_get_buf_size(void UNUSED *elem, hid_t type_id, hsize_t UNUSED ndim, hssize_t *point, void *op_data) { H5T_vlen_bufsize_t *vlen_bufsize=(H5T_vlen_bufsize_t *)op_data; H5T_t *dt = NULL; herr_t ret_value=0; /* The correct return value, if this function succeeds */ FUNC_ENTER_NOAPI(H5D_vlen_get_buf_size, FAIL); assert(op_data); assert(H5I_DATATYPE == H5I_get_type(type_id)); /* Check args */ if (NULL==(dt=H5I_object(type_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); /* Make certain there is enough fixed-length buffer available */ if ((vlen_bufsize->fl_tbuf=H5FL_BLK_REALLOC(vlen_fl_buf,vlen_bufsize->fl_tbuf,H5T_get_size(dt)))==NULL) 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,1,(const hssize_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(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 * data from the dataset, using the space_id for the selection in the * dataset on disk and the type_id for the memory representation of the * VL data, in memory. The *size value is modified according to how many * bytes are required to store the VL data in memory. * * Implementation: This routine actually performs the read with a custom * memory manager which basically just counts the bytes requested and * 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 * Wednesday, August 11, 1999 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id, hsize_t *size) { H5T_vlen_bufsize_t vlen_bufsize = {0, 0, 0, 0, 0, 0, 0}; char bogus; /* bogus value to pass to H5Diterate() */ H5P_genclass_t *pclass; /* Property class */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value=FAIL; FUNC_ENTER_API(H5Dvlen_get_buf_size, FAIL); H5TRACE4("e","iii*h",dataset_id,type_id,space_id,size); /* Check args */ if (H5I_DATASET!=H5I_get_type(dataset_id) || H5I_DATATYPE!=H5I_get_type(type_id) || H5I_DATASPACE!=H5I_get_type(space_id) || size==NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument"); /* Save the dataset ID */ vlen_bufsize.dataset_id=dataset_id; /* Get a copy of the dataspace ID */ if((vlen_bufsize.fspace_id=H5Dget_space(dataset_id))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "can't copy dataspace"); /* Create a scalar for the memory dataspace */ if((vlen_bufsize.mspace_id=H5Screate(H5S_SCALAR))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "can't create dataspace"); /* Grab the temporary buffers required */ if((vlen_bufsize.fl_tbuf=H5FL_BLK_ALLOC(vlen_fl_buf,1,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available"); if((vlen_bufsize.vl_tbuf=H5FL_BLK_ALLOC(vlen_vl_buf,1,0))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available"); /* Get the pointer to the dataset transfer class */ if (NULL == (pclass = H5I_object(H5P_CLS_DATASET_XFER_g))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list class"); /* Change to the custom memory allocation routines for reading VL data */ if((vlen_bufsize.xfer_pid=H5P_create_id(pclass))<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTCREATE, FAIL, "no dataset xfer plists available"); /* Get the property list struct */ if (NULL == (plist = H5I_object(vlen_bufsize.xfer_pid))) 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) HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't set VL data allocation routine"); /* Set the initial number of bytes required */ vlen_bufsize.size=0; /* Call H5Diterate with args, etc. */ ret_value=H5Diterate(&bogus,type_id,space_id,H5D_vlen_get_buf_size,&vlen_bufsize); /* Get the size if we succeeded */ if(ret_value>=0) *size=vlen_bufsize.size; done: if(vlen_bufsize.fspace_id>0) H5Sclose(vlen_bufsize.fspace_id); if(vlen_bufsize.mspace_id>0) H5Sclose(vlen_bufsize.mspace_id); if(vlen_bufsize.fl_tbuf!=NULL) H5FL_BLK_FREE(vlen_fl_buf,vlen_bufsize.fl_tbuf); if(vlen_bufsize.vl_tbuf!=NULL) H5FL_BLK_FREE(vlen_vl_buf,vlen_bufsize.vl_tbuf); if(vlen_bufsize.xfer_pid>0) H5I_dec_ref(vlen_bufsize.xfer_pid); FUNC_LEAVE(ret_value); } /* end H5Dvlen_get_buf_size() */ /*-------------------------------------------------------------------------- NAME H5D_fill PURPOSE Fill a selection in memory with a value (internal version) USAGE herr_t H5Dfill(fill, fill_type, buf, buf_type, space) const void *fill; IN: Pointer to fill value to use H5T_t *fill_type; IN: Datatype of the fill value void *buf; IN/OUT: Memory buffer to fill selection within H5T_t *buf_type; IN: Datatype of the elements in buffer H5S_t *space; IN: Dataspace describing memory buffer & containing selection to use. RETURNS Non-negative on success/Negative on failure. DESCRIPTION Use the selection in the dataspace to fill elements in a memory buffer. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS If "fill" parameter is NULL, use all zeros as fill value. If "fill_type" parameter is NULL, use "buf_type" for the fill value datatype. EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space) { H5T_path_t *tpath = NULL; /* Conversion information*/ uint8_t *tconv_buf = NULL; /* Data type conv buffer */ uint8_t *bkg_buf = NULL; /* Temp conversion buffer */ hid_t src_id = -1, dst_id = -1; /* Temporary type IDs */ size_t src_type_size; /* Size of source type */ size_t dst_type_size; /* Size of destination type*/ size_t buf_size; /* Desired buffer size */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_fill); /* Check args */ assert(buf); assert(buf_type); assert(space); /* Check for "default" fill value */ if(fill_type==NULL) fill_type=buf_type; /* Get the memory and file datatype sizes */ src_type_size = H5T_get_size(fill_type); dst_type_size = H5T_get_size(buf_type); /* Get the maximum buffer size needed and allocate it */ buf_size=MAX(src_type_size,dst_type_size); if (NULL==(tconv_buf = H5FL_BLK_ALLOC(type_elem,buf_size,0)) || NULL==(bkg_buf = H5FL_BLK_ALLOC(type_elem,buf_size,1))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); /* Copy the user's data into the buffer for conversion */ if(fill==NULL) HDmemset(tconv_buf,0,src_type_size); else HDmemcpy(tconv_buf,fill,src_type_size); /* Convert memory buffer into disk buffer */ /* Set up type conversion function */ if (NULL == (tpath = H5T_path_find(fill_type, buf_type, NULL, NULL))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } else if (!H5T_IS_NOOP(tpath)) { if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(fill_type, H5T_COPY_ALL)))<0 || (dst_id = H5I_register(H5I_DATATYPE, H5T_copy(buf_type, H5T_COPY_ALL)))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); } /* Perform data type conversion */ if (H5T_convert(tpath, src_id, dst_id, (hsize_t)1, 0, 0, tconv_buf, bkg_buf, H5P_DEFAULT)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed"); /* Fill the selection in the memory buffer */ if(H5S_select_fill(tconv_buf, dst_type_size, space, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed"); done: if (tconv_buf) H5FL_BLK_FREE(type_elem,tconv_buf); if (bkg_buf) H5FL_BLK_FREE(type_elem,bkg_buf); FUNC_LEAVE (ret_value); } /* H5D_fill() */ /*-------------------------------------------------------------------------- NAME H5Dfill PURPOSE Fill a selection in memory with a value USAGE herr_t H5Dfill(fill, fill_type, space, buf, buf_type) const void *fill; IN: Pointer to fill value to use hid_t fill_type_id; IN: Datatype of the fill value void *buf; IN/OUT: Memory buffer to fill selection within hid_t buf_type_id; IN: Datatype of the elements in buffer hid_t space_id; IN: Dataspace describing memory buffer & containing selection to use. RETURNS Non-negative on success/Negative on failure. DESCRIPTION Use the selection in the dataspace to fill elements in a memory buffer. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS If "fill" parameter is NULL, use all zeros as fill value EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t H5Dfill(const void *fill, hid_t fill_type_id, void *buf, hid_t buf_type_id, hid_t space_id) { H5S_t *space; /* Dataspace */ H5T_t *fill_type; /* Fill-value datatype */ H5T_t *buf_type; /* Buffer datatype */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dfill, FAIL); H5TRACE5("e","xixii",fill,fill_type_id,buf,buf_type_id,space_id); /* Check args */ if (buf==NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer"); if (NULL == (space=H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataspace"); if (NULL == (fill_type=H5I_object_verify(fill_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype"); if (NULL == (buf_type=H5I_object_verify(buf_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype"); /* Fill the selection in the memory buffer */ if(H5D_fill(fill,fill_type,buf,buf_type,space)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed"); done: FUNC_LEAVE (ret_value); } /* H5Dfill() */ /*------------------------------------------------------------------------- * Function: H5Dset_extent * * Purpose: Modifies the dimensions of a dataset, based on H5Dextend. * Can change to a lower dimension. * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * Robb Matzke * * Date: April 9, 2002 * * Comments: Public function, calls private H5D_set_extent * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dset_extent(hid_t dset_id, const hsize_t *size) { H5D_t *dset = NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dset_extent, FAIL); H5TRACE2("e","i*h",dset_id,size); /* Check args */ if(NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if(!size) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified"); /* Private function */ if(H5D_set_extent(dset, size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set extend dataset"); done: FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_set_extent * * Purpose: Based in H5D_extend, allows change to a lower dimension, * calls H5S_set_extent and H5F_istore_prune_by_extent instead * * Return: Success: 0, Failure: -1 * * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu * Robb Matzke * * Date: April 9, 2002 * * Comments: Private function * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_set_extent(H5D_t *dset, const hsize_t *size) { hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Current dimension sizes */ int rank; /* Dataspace # of dimensions */ herr_t ret_value = SUCCEED; /* Return value */ H5S_t *space = NULL; H5P_genplist_t *plist; H5D_alloc_time_t alloc_time; /* When to allocate raw data space */ int u; unsigned shrink = 0; /* Flag to indicate a dimension has shrank */ unsigned expand = 0; /* Flag to indicate a dimension has grown */ int changed = 0; FUNC_ENTER_NOAPI(H5D_set_extent, FAIL); /* Check args */ assert(dset); assert(size); /*------------------------------------------------------------------------- * Get the data space *------------------------------------------------------------------------- */ if(NULL == (space = H5S_read(&(dset->ent)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space info from dset header"); /*------------------------------------------------------------------------- * 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"); for(u = 0; u < rank; u++) { if(size[u] < curr_dims[u]) shrink = 1; if(size[u] > curr_dims[u]) expand = 1; } /*------------------------------------------------------------------------- * 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) { /* Get the dataset creation property list */ if(NULL == (plist = H5I_object(dset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dset creation property list"); if(H5P_get(plist, H5D_CRT_ALLOC_TIME_NAME, &alloc_time) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't retrieve space allocation time"); /*------------------------------------------------------------------------- * Modify the dataset storage *------------------------------------------------------------------------- */ /* Save the new dataspace in the file if necessary */ if(H5S_modify(&(dset->ent), space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); /* Allocate space for the new parts of the dataset, if appropriate */ if(expand && alloc_time==H5D_ALLOC_TIME_EARLY) if(H5D_alloc_storage(dset->ent.file, dset, H5D_ALLOC_EXTEND) < 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->layout.type) { /* Remove excess chunks */ if(H5F_istore_prune_by_extent(dset->ent.file, &dset->layout, space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks "); /* Reset the elements outsize the new dimensions, but in existing chunks */ if(H5F_istore_initialize_by_extent(dset->ent.file, &dset->layout, plist, space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to initialize chunks "); } /* end if */ } /* end if */ done: if(space) H5S_close(space); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_flush * * Purpose: Flush any compact datasets cached in memory * * Return: Success: Non-negative * Failure: Negative * * * Programmer: Ray Lu * * Date: August 14, 2002 * * Comments: Private function * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5D_flush(H5F_t *f) { unsigned num_dsets; /* Number of datasets in file */ hid_t *id_list=NULL; /* list of dataset IDs */ H5D_t *dataset=NULL; /* Dataset pointer */ herr_t ret_value = SUCCEED; /* Return value */ unsigned j; /* Index variable */ FUNC_ENTER_NOAPI(H5D_flush, FAIL); /* Check args */ assert(f); /* Update layout message for compact dataset */ if(H5F_get_obj_count(f, H5F_OBJ_DATASET, &num_dsets)<0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset number"); if(num_dsets>0) { if(NULL==(id_list=H5MM_malloc(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, id_list)<0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to get dataset ID list"); for(j=0; jlayout.type==H5D_COMPACT && dataset->layout.dirty) if(H5O_modify(&(dataset->ent), H5O_LAYOUT, 0, 0, &(dataset->layout))<0) HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to update layout message"); dataset->layout.dirty = FALSE; } } done: if(id_list!=NULL) H5MM_xfree(id_list); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * 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 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Ddebug(hid_t dset_id, unsigned UNUSED flags) { H5D_t *dset=NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Ddebug, FAIL); H5TRACE2("e","iIu",dset_id,flags); /* Check args */ if (NULL==(dset=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->layout.type) { H5F_istore_dump_btree(dset->ent.file, stdout, dset->layout.ndims, dset->layout.addr); } else if (H5D_CONTIGUOUS==dset->layout.type) { HDfprintf(stdout, " %-10s %a\n", "Address:", dset->layout.addr); } done: FUNC_LEAVE(ret_value); }