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author	Honglei Zhang <honglei.zhang@nokia.com>	2011-04-19 14:29:27 (GMT)
committer	Honglei Zhang <honglei.zhang@nokia.com>	2011-04-19 14:29:27 (GMT)
commit	986ab48f1128bdd56fa408fca8f4a564e874dd4d (patch)
tree	46d5e20dbf23fbbc0d95b0a4bf111f301a45fa99 /tests
parent	6dcb0028e44cba2a00c2fb867fb1757ad5b1a254 (diff)
download	Qt-986ab48f1128bdd56fa408fca8f4a564e874dd4d.zip Qt-986ab48f1128bdd56fa408fca8f4a564e874dd4d.tar.gz Qt-986ab48f1128bdd56fa408fca8f4a564e874dd4d.tar.bz2

Fix memory leak bugs in XmlPatterns

In XmlPatterns implementation, QExplicitlySharedDataPointer and QSharedData classes are widely used. The over use of these classes has cuased couple of cyclic references. Some codes are refactored to use plain C++ pointer to break the reference loop. Task-number: QTBUG-15191 Reviewed-by: Laszlo Agocs and Sami Merila

Diffstat (limited to 'tests')

-rw-r--r--

tests/auto/qxmlquery/tst_qxmlquery.cpp

-rw-r--r--

tests/auto/xmlpatternsdiagnosticsts/xmlpatternsdiagnosticsts.pro

-rw-r--r--

tests/auto/xmlpatternsschemats/xmlpatternsschemats.pro

-rw-r--r--

tests/auto/xmlpatternsxqts/xmlpatternsxqts.pro

4 files changed, 8 insertions, 2 deletions

/**************************************************************************** * 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 "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*/ #define PABLO_MASK H5D_mask /* * 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 */ }; static int interface_initialize_g = 0; #define INTERFACE_INIT H5D_init_interface static herr_t H5D_init_interface(void); static herr_t H5D_init_storage(H5D_t *dataset, const H5S_t *space); 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_STATIC(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) { FUNC_ENTER_NOAPI(H5D_init, FAIL); /* FUNC_ENTER() does all the work */ FUNC_LEAVE(SUCCEED); } /*-------------------------------------------------------------------------- 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_space_time_t space_time = H5D_CRT_SPACE_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_SPACE_TIME_NAME, H5D_CRT_SPACE_TIME_SIZE, &space_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 (TRUE!=H5P_isa_class(new_plist_id,H5P_DATASET_CREATE) || NULL == (new_plist = H5I_object(new_plist_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if (TRUE!=H5P_isa_class(old_plist_id,H5P_DATASET_CREATE) || NULL == (old_plist = H5I_object(old_plist_id))) 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 (TRUE!=H5P_isa_class(dcpl_id,H5P_DATASET_CREATE) || NULL == (plist = H5I_object(dcpl_id))) 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 (TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (plist = H5I_object(dxpl_id))) 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 (TRUE!=H5P_isa_class(dxpl_id,H5P_DATASET_XFER) || NULL == (plist = H5I_object(dxpl_id))) 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(H5I_GENPROP_LST != H5I_get_type(plist_id) || 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 (H5I_GENPROP_LST != H5I_get_type(plist_id) || 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 (H5I_GENPROP_LST != H5I_get_type(plist_id) || 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 *ret_value = NULL; /*return value */ FUNC_ENTER_NOAPI(H5D_new, NULL); /* check args */ /* Nothing to check */ if (NULL==(ret_value = 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; if(TRUE != H5P_isa_class(dcpl_id, H5P_DATASET_CREATE)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not property list"); /* Check arguments. */ if (NULL == (plist = H5I_object(dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a property list"); ret_value->dcpl_id = H5P_copy_plist(plist); ret_value->ent.header = HADDR_UNDEF; /* Success */ done: 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; 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_space_time_t space_time; H5D_fill_time_t fill_time; H5O_fill_t fill_prop={NULL,0,NULL}; H5O_fill_new_t fill={NULL, 0, NULL, H5D_SPACE_ALLOC_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); assert (TRUE==H5P_isa_class(dcpl_id,H5P_DATASET_CREATE)); /* Get property list object */ if (NULL == (plist = H5I_object(dcpl_id))) 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"); /* 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"); #ifdef H5_HAVE_PARALLEL /* 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"); #endif /*H5_HAVE_PARALLEL*/ 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"); 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); switch (dcpl_layout) { 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; i<ndims; i++) { if (max_dim[i]>new_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; u<new_dset->layout.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; u<new_dset->layout.ndims-1; u++) new_dset->layout.dim[u] = chunk_size[u]; 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_SPACE_TIME_NAME, &space_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.space_time = space_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"); /* * Initialize storage. We assume that external storage is already * initialized by the caller, or at least will be before I/O is performed. * For parallelization, space is always allocated now except using * external storage. For contiguous layout, space is allocated now if * space allocate time is early; otherwise delay allocation until H5Dwrite. */ #ifdef H5_HAVE_PARALLEL if (0==efl.nused) { if(H5F_arr_create(f, &(new_dset->layout))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); } /* end if */ else new_dset->layout.addr = HADDR_UNDEF; #else /*H5_HAVE_PARALLEL*/ if (0==efl.nused) { if(dcpl_layout==H5D_CHUNKED || (dcpl_layout==H5D_CONTIGUOUS && space_time==H5D_SPACE_ALLOC_EARLY)) { if (H5F_arr_create(f, &(new_dset->layout))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); } /* end if */ else new_dset->layout.addr = HADDR_UNDEF; } /* end if */ else new_dset->layout.addr = HADDR_UNDEF; #endif /*H5_HAVE_PARALLEL*/ /* Update layout message */ if (H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, 0, &(new_dset->layout))<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update layout message"); /* Update external storage message */ if (efl.nused>0) { size_t heap_size = H5HL_ALIGN (1); for (i=0; i<efl.nused; i++) heap_size += H5HL_ALIGN (HDstrlen (efl.slot[i].name)+1); if (H5HL_create (f, heap_size, &(efl.heap_addr)/*out*/)<0 || (size_t)(-1)==H5HL_insert(f, efl.heap_addr, 1, "")) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to create external file list name heap"); for (i=0; i<efl.nused; i++) { size_t offset = H5HL_insert(f, efl.heap_addr, HDstrlen(efl.slot[i].name)+1, efl.slot[i].name); assert(0==efl.slot[i].name_offset); if ((size_t)(-1)==offset) HGOTO_ERROR(H5E_EFL, H5E_CANTINIT, NULL, "unable to insert URL into name heap"); efl.slot[i].name_offset = offset; } /* end for */ if (H5O_modify (&(new_dset->ent), H5O_EFL, 0, H5O_FLAG_CONSTANT, &efl)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update external file list message"); } /* end if */ /* Initialize the raw data when it's * 1. Parallel I/O * 2. layout is contiguous, space allocation time is early, fill value * writing time is upon allocation * 3. external space is treated the same as internal except it's always * assumed as early for space allocation time. */ #ifdef H5_HAVE_PARALLEL if (H5D_init_storage(new_dset, space)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); #else /*H5_HAVE_PARALLEL*/ if(fill_time==H5D_FILL_TIME_ALLOC && ((space_time==H5D_SPACE_ALLOC_EARLY && !efl.nused) || (efl.nused))) if (H5D_init_storage(new_dset, space)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); #endif /*H5_HAVE_PARALLEL*/ /* 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 * *------------------------------------------------------------------------- */ 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: 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. * *------------------------------------------------------------------------- */ H5D_t * H5D_open_oid(H5G_entry_t *ent) { H5D_t *dataset = NULL; /*new dataset struct */ H5D_t *ret_value = NULL; /*return value */ H5S_t *space = NULL; /*data space */ H5O_fill_new_t fill = {NULL, 0, NULL, H5D_SPACE_ALLOC_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"); /* Copy over the symbol table information if it's provided */ HDmemcpy(&(dataset->ent),ent,sizeof(H5G_entry_t)); /* 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"); if (NULL==(space=H5S_read (&(dataset->ent)))) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to read data space 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"); /* 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)); } 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_SPACE_TIME_NAME, &fill.space_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 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"); #ifdef H5_HAVE_PARALLEL /* 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"); #endif /*H5_HAVE_PARALLEL*/ /* * 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; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* end switch */ /* Get the external file list message, which might not exist. Space is * also undefined when space allocate time is H5D_SPACE_ALLOC_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 for chunked datasets. * This is especially important for parallel I/O where the B-tree must * be fully populated before I/O can happen. */ if ((H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR) && H5D_CHUNKED==dataset->layout.type) { if (H5D_init_storage(dataset, space)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize file storage"); } /* Success */ ret_value = dataset; done: if (space) H5S_close(space); 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); /* 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; 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_<foo>_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); assert(H5I_GENPROP_LST==H5I_get_type(dxpl_id)); assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); /* 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 = H5I_object_verify(dxpl_id,H5I_GENPROP_LST))) 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(nelmts > 0 && efl.nused==0 && dataset->layout.type==H5D_CONTIGUOUS && 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); 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_start<nelmts; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ assert((*file_space->select.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_<foo>_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 */ 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); assert(H5I_GENPROP_LST==H5I_get_type(dxpl_id)); assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); /* 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 = H5I_object_verify(dxpl_id,H5I_GENPROP_LST))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); #ifdef H5_HAVE_PARALLEL /* 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"); #endif /*H5_HAVE_PARALLEL*/ #ifdef H5_HAVE_PARALLEL /* 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"); #endif /*H5_HAVE_PARALLEL*/ if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR)) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file"); 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 driver 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_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"); /* Allocate data space and initialize it if it hasn't been. Also modify * header message for layout(this is only for forward compatibility). */ if(nelmts > 0 && efl.nused==0 && dataset->layout.type==H5D_CONTIGUOUS && dataset->layout.addr==HADDR_UNDEF) { /* Allocate storage */ if(H5F_arr_create(dataset->ent.file, &(dataset->layout))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage"); /* Initialize raw data */ if(fill_time==H5D_FILL_TIME_ALLOC) if(H5D_init_storage(dataset, file_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize dataset with fill value"); /* Update layout message */ if (H5O_modify (&(dataset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT, &(dataset->layout)) < 0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout message"); } /* 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_start<nelmts; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ assert((*file_space->select.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) { herr_t changed, ret_value=SUCCEED; H5S_t *space = NULL; H5O_fill_t fill; H5P_genplist_t *plist; /* Property list */ FUNC_ENTER_NOAPI(H5D_extend, FAIL); /* Check args */ assert (dataset); assert (size); /* * 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"); /* Initialize the new parts of the dataset */ #ifdef LATER if (H5S_select_all(space)<0 || H5S_select_hyperslab(space, H5S_SELECT_DIFF, zero, NULL, old_dims, NULL)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to select new extents for fill value"); #else /* * We don't have the H5S_SELECT_DIFF operator yet. We really only * need it for contiguous datasets because the chunked datasets will * either fill on demand during I/O or attempt a fill of all chunks. */ 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_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value"); if(H5D_CONTIGUOUS == dataset->layout.type && fill.buf) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to select fill value region"); #endif if (H5D_init_storage(dataset, space)<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_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, const H5S_t *space) { hssize_t snpoints; /* Number of points in space (for error checking) */ size_t npoints; /* Number of points in space */ size_t ptsperbuf; /* Maximum # of points which fit in the buffer */ size_t bufsize=64*1024; /* Size of buffer to write */ size_t size; /* Current # of points to write */ hsize_t addr; /* Offset in dataset */ void *buf = NULL; /* Buffer for fill value writing */ H5O_fill_t fill; /* Fill value information */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_init_storage); assert(dset); assert(space); /* 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"); switch (dset->layout.type) { case H5D_CONTIGUOUS: /* * If the fill value is set then write it to the entire extent * of the dataset. */ snpoints = H5S_get_simple_extent_npoints(space); assert(snpoints>=0); H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); if (fill.buf) { /* * Fill the entire current extent with the fill value. We can do * this quite efficiently by making sure we copy the fill value * in relatively large pieces. */ ptsperbuf = MAX(1, bufsize/fill.size); bufsize = ptsperbuf*fill.size; /* Allocate temporary buffer */ if ((buf=H5FL_BLK_ALLOC(type_conv,bufsize,0))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer"); /* Fill the buffer with the fill value */ H5V_array_fill(buf, fill.buf, fill.size, ptsperbuf); /* Start at the beginning of the dataset */ addr = 0; /* Loop through writing the fill value to the dataset */ while (npoints>0) { size = MIN(ptsperbuf, npoints) * fill.size; if (H5F_seq_write(dset->ent.file, H5P_DATASET_XFER_DEFAULT, &(dset->layout), plist, space, fill.size, size, addr, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); npoints -= MIN(ptsperbuf, npoints); addr += size; } /* end while */ } /* end if */ break; case H5D_CHUNKED: #ifdef H5_HAVE_PARALLEL /* * If the dataset is accessed via parallel I/O, allocate file space * for all chunks now and initialize each chunk with the fill value. */ if (IS_H5FD_MPIO(dset->ent.file) || IS_H5FD_MPIPOSIX(dset->ent.file)) { /* 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]; 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 */ #endif /*H5_HAVE_PARALLEL*/ break; } /* end switch */ done: if (buf) H5FL_BLK_FREE(type_conv,buf); 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=0; FUNC_ENTER_NOAPI(H5D_get_storage_size, 0); if (H5D_CHUNKED==dset->layout.type) { ret_value = H5F_istore_allocated(dset->ent.file, dset->layout.ndims, dset->layout.addr); } else { /* Sanity Check */ assert(dset->layout.type==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; u<dset->layout.ndims; u++) ret_value *= dset->layout.dim[u]; } /* end else */ } /* end else */ 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; 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; FUNC_LEAVE(vlen_bufsize->vl_tbuf); } /* 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; int u; int shrink = 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 in 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; break; } } /*------------------------------------------------------------------------- * Modify the size of the data space *------------------------------------------------------------------------- */ if(H5S_set_extent(space, size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space"); /*------------------------------------------------------------------------- * 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"); /* Initialize the new parts of the dset */ if(H5D_init_storage(dset, space) < 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 "); /* 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"); /* 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 */ done: if(space) H5S_close(space); 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); }


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