/**************************************************************************** * 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. * * * ****************************************************************************/ /* $Id$ */ #include "H5private.h" /* Generic Functions */ #include "H5Iprivate.h" /* IDs */ #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 "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ #include "H5Sprivate.h" /* Dataspace functions rky 980813 */ #include "H5Vprivate.h" /* Vector and array functions */ #include "H5Zprivate.h" /* Data filters */ /* * The MPIO driver is needed because there are kludges in this file and * places where we check for things that aren't handled by this driver. */ #include "H5FDmpio.h" #ifdef H5_HAVE_PARALLEL /* Remove this if H5R_DATASET_REGION is no longer used in this file */ # include "H5Rpublic.h" #endif #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 */ H5D_create_t *create_parms; /*creation parameters */ H5O_layout_t layout; /*data layout */ }; /* Default dataset creation property list */ const H5D_create_t H5D_create_dflt = { H5D_CONTIGUOUS, /* Layout */ 1, /* Chunk dimensions */ {1, 1, 1, 1, 1, 1, 1, 1, /* Chunk size. These default values....*/ 1, 1, 1, 1, 1, 1, 1, 1, /*...are quite useless. Larger chunks..*/ 1, 1, 1, 1, 1, 1, 1, 1, /*...produce fewer, but larger I/O......*/ 1, 1, 1, 1, 1, 1, 1, 1}, /*...requests. */ /* Fill value */ {NULL, 0, NULL}, /* No fill value */ /* External file list */ {HADDR_UNDEF, /* External file list heap address */ 0, /*...slots allocated */ 0, /*...slots used */ NULL}, /*...slot array */ /* Filters */ {0, 0, NULL} /* No filters in pipeline */ }; /* Interface initialization? */ 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(const H5D_create_t *create_parms); /* 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 background conversion data */ H5FL_BLK_DEFINE_STATIC(bkgr_conv); /* Declare a free list to manage blocks of fill conversion data */ H5FL_BLK_DEFINE_STATIC(fill_conv); /* 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(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. --------------------------------------------------------------------------*/ static herr_t H5D_init_interface(void) { H5P_genclass_t *pclass; /* Property list class to modify */ size_t def_max_temp_buf=H5D_XFER_MAX_TEMP_BUF_DEF; /* Default value for maximum temp buffer size */ void *def_tconv_buf=H5D_XFER_TCONV_BUF_DEF; /* Default value for type conversion buffer */ void *def_bkgr_buf=H5D_XFER_BKGR_BUF_DEF; /* Default value for background buffer */ H5T_bkg_t def_bkgr_buf_type=H5D_XFER_BKGR_BUF_TYPE_DEF; /* Default value for background buffer type */ double def_btree_split_ratio[3]=H5D_XFER_BTREE_SPLIT_RATIO_DEF; /* Default value for B-tree node split ratios */ unsigned def_hyper_cache=H5D_XFER_HYPER_CACHE_DEF; /* Default value for hyperslab caching */ unsigned def_hyper_cache_lim=H5D_XFER_HYPER_CACHE_LIM_DEF; /* Default value for hyperslab cache limit */ H5MM_allocate_t def_vlen_alloc=H5D_XFER_VLEN_ALLOC_DEF; /* Default value for vlen allocation function */ void *def_vlen_alloc_info=H5D_XFER_VLEN_ALLOC_INFO_DEF; /* Default value for vlen allocation information */ H5MM_free_t def_vlen_free=H5D_XFER_VLEN_FREE_DEF; /* Default value for vlen free function */ void *def_vlen_free_info=H5D_XFER_VLEN_FREE_INFO_DEF; /* Default value for vlen free information */ hid_t def_vfl_id=H5D_XFER_VFL_ID_DEF; /* Default value for file driver ID */ void *def_vfl_info=H5D_XFER_VFL_INFO_DEF; /* Default value for file driver info */ #ifdef COALESCE_READS unsigned def_gather_reads=H5D_XFER_GATHER_READS_DEF; /* Default value for 'gather reads' property */ #endif /* COALESCE_READS */ size_t def_hyp_vec_size=H5D_XFER_HYPER_VECTOR_SIZE_DEF; /* Default value for vector size */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER(H5D_init_interface, FAIL); /* 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"); } /* Register the default dataset creation properties */ assert(H5P_CLS_DATASET_XFER_g!=(-1)); /* Get the pointer to the dataset creation class */ if (H5I_GENPROP_CLS != H5I_get_type(H5P_CLS_DATASET_XFER_g) || NULL == (pclass = H5I_object(H5P_CLS_DATASET_XFER_g))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list class"); /* Register the max. temp buffer size property */ if(H5P_register(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(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(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(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(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"); /* Register the hyperslab caching property */ if(H5P_register(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(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"); /* Register the vlen allocation function property */ if(H5P_register(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(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(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(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(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(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"); #ifdef COALESCE_READS /* Register the 'gather reads' property */ if(H5P_register(pclass,H5D_XFER_GATHER_READS_NAME,H5D_XFER_GATHER_READS_SIZE,&def_gather_reads,NULL,NULL,NULL,NULL,NULL)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class"); #endif /* COALESCE_READS */ /* Register the vector size property */ if(H5P_register(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"); /* Register the default data transfer property list */ if ((H5P_LST_DATASET_XFER_g = H5Pcreate_list (H5P_CLS_DATASET_XFER_g))<0) HRETURN_ERROR (H5E_PLIST, H5E_CANTREGISTER, FAIL, "can't register default property list"); 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; 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*/ } } return n; } /*------------------------------------------------------------------------- * 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 */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER(H5D_xfer_create, FAIL); /* Get the driver information */ if(H5P_get(dxpl_id, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID"); if(H5P_get(dxpl_id, 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(dxpl_id, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTSET, FAIL, "Can't set VFL driver ID"); if(H5P_set(dxpl_id, 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_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 */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER(H5D_xfer_close, FAIL); if(H5Pget(dxpl_id, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID"); if(H5Pget(dxpl_id, 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 = FAIL; const H5D_create_t *create_parms = NULL; FUNC_ENTER(H5Dcreate, FAIL); H5TRACE5("i","isiii",loc_id,name,type_id,space_id,plist_id); /* Check arguments */ if (NULL == (loc = H5G_loc(loc_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location"); } if (!name || !*name) { HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name"); } if (H5I_DATATYPE != H5I_get_type(type_id) || NULL == (type = H5I_object(type_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a type"); } if (H5I_DATASPACE != H5I_get_type(space_id) || NULL == (space = H5I_object(space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } if (H5P_DEFAULT==plist_id) { create_parms = &H5D_create_dflt; } else if (H5P_DATASET_CREATE != H5P_get_class(plist_id) || NULL == (create_parms = H5I_object(plist_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); } /* build and open the new dataset */ if (NULL == (new_dset = H5D_create(loc, name, type, space, create_parms))) { HRETURN_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) { H5D_close(new_dset); HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataset"); } 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 = FAIL; FUNC_ENTER(H5Dopen, FAIL); H5TRACE2("i","is",loc_id,name); /* Check args */ if (NULL == (loc = H5G_loc(loc_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location"); } if (!name || !*name) { HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name"); } /* Find the dataset */ if (NULL == (dataset = H5D_open(loc, name))) { HRETURN_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "dataset not found"); } /* Create an atom for the dataset */ if ((ret_value = H5I_register(H5I_DATASET, dataset)) < 0) { H5D_close(dataset); HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register dataset"); } 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 */ FUNC_ENTER(H5Dclose, FAIL); H5TRACE1("e","i",dset_id); /* Check args */ if (H5I_DATASET != H5I_get_type(dset_id) || NULL == (dset = H5I_object(dset_id)) || NULL == dset->ent.file) { HRETURN_ERROR(H5E_ARGS, 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) { HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't free"); } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * 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 = FAIL; FUNC_ENTER (H5Dget_space, FAIL); H5TRACE1("i","i",dset_id); /* Check args */ if (H5I_DATASET!=H5I_get_type (dset_id) || NULL==(dset=H5I_object (dset_id))) { HRETURN_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))) { HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get data space"); } /* Create an atom */ if ((ret_value=H5I_register (H5I_DATASPACE, space))<0) { H5S_close(space); HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register data space"); } 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 = NULL; FUNC_ENTER(H5D_get_space, NULL); assert(dset); if (NULL==(space=H5S_read(&(dset->ent)))) { HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to load space info from dataset header"); } FUNC_LEAVE(space); } /*------------------------------------------------------------------------- * 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 (H5Dget_type, FAIL); H5TRACE1("i","i",dset_id); /* Check args */ if (H5I_DATASET!=H5I_get_type (dset_id) || NULL==(dset=H5I_object (dset_id))) { HRETURN_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))) { HRETURN_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) { HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid VL location"); } if (H5T_lock (copied_type, FALSE)<0) { H5T_close (copied_type); HRETURN_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) { H5T_close (copied_type); HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register data type"); } 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 H5Pclose(). * * Failure: FAIL * * Programmer: Robb Matzke * Tuesday, February 3, 1998 * * Modifications: * *------------------------------------------------------------------------- */ hid_t H5Dget_create_plist(hid_t dset_id) { H5D_t *dset = NULL; H5D_create_t *copied_parms = NULL; hid_t ret_value = FAIL; FUNC_ENTER (H5Dget_create_plist, FAIL); H5TRACE1("i","i",dset_id); /* Check args */ if (H5I_DATASET!=H5I_get_type (dset_id) || NULL==(dset=H5I_object (dset_id))) { HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } /* Copy the creation property list */ if (NULL==(copied_parms=H5P_copy (H5P_DATASET_CREATE, dset->create_parms))) { HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy the creation property list"); } /* Copy the dataset type into the fill value message */ if (!copied_parms->fill.type && NULL==(copied_parms->fill.type=H5T_copy(dset->type, H5T_COPY_TRANSIENT))) { HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy dataset data type for fill value"); } /* Create an atom */ if ((ret_value=H5I_register ((H5I_type_t)(H5I_TEMPLATE_0+ H5P_DATASET_CREATE), copied_parms))<0) { HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register creation property list"); } 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; FUNC_ENTER(H5Dread, FAIL); H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id, plist_id,buf); /* check arguments */ if (H5I_DATASET != H5I_get_type(dset_id) || NULL == (dset = H5I_object(dset_id)) || NULL == dset->ent.file) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } if (H5I_DATATYPE != H5I_get_type(mem_type_id) || NULL == (mem_type = H5I_object(mem_type_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); } if (H5S_ALL != mem_space_id) { if (H5I_DATASPACE != H5I_get_type(mem_space_id) || NULL == (mem_space = H5I_object(mem_space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } /* Check for valid selection */ if(H5S_select_valid(mem_space)!=TRUE) { HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } } if (H5S_ALL != file_space_id) { if (H5I_DATASPACE != H5I_get_type(file_space_id) || NULL == (file_space = H5I_object(file_space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } /* Check for valid selection */ if(H5S_select_valid(file_space)!=TRUE) { HRETURN_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!=H5Pisa_class(plist_id,H5P_DATASET_XFER)) HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); if (!buf) HRETURN_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) HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data"); FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * 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; FUNC_ENTER(H5Dwrite, FAIL); H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id, plist_id,buf); /* check arguments */ if (H5I_DATASET != H5I_get_type(dset_id) || NULL == (dset = H5I_object(dset_id)) || NULL == dset->ent.file) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } if (H5I_DATATYPE != H5I_get_type(mem_type_id) || NULL == (mem_type = H5I_object(mem_type_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); } if (H5S_ALL != mem_space_id) { if (H5I_DATASPACE != H5I_get_type(mem_space_id) || NULL == (mem_space = H5I_object(mem_space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } /* Check for valid selection */ if (H5S_select_valid(mem_space)!=TRUE) { HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } } if (H5S_ALL != file_space_id) { if (H5I_DATASPACE != H5I_get_type(file_space_id) || NULL == (file_space = H5I_object(file_space_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); } /* Check for valid selection */ if (H5S_select_valid(file_space)!=TRUE) { HRETURN_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!=H5Pisa_class(plist_id,H5P_DATASET_XFER)) HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); if (!buf) HRETURN_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) HRETURN_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data"); FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * 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; FUNC_ENTER (H5Dextend, FAIL); H5TRACE2("e","i*h",dset_id,size); /* Check args */ if (H5I_DATASET!=H5I_get_type(dset_id) || NULL==(dset=H5I_object(dset_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } if (!size) { HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified"); } /* Increase size */ if (H5D_extend (dset, size)<0) { HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to extend dataset"); } FUNC_LEAVE (SUCCEED); } /*------------------------------------------------------------------------- * 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: * *------------------------------------------------------------------------- */ H5D_t * H5D_new(const H5D_create_t *create_parms) { H5D_t *ret_value = NULL; /*return value */ FUNC_ENTER(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(create_parms!=NULL) { ret_value->create_parms = H5P_copy (H5P_DATASET_CREATE, create_parms); } else { ret_value->create_parms = H5P_copy (H5P_DATASET_CREATE, &H5D_create_dflt); } 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. *------------------------------------------------------------------------- */ H5D_t * H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type, const H5S_t *space, const H5D_create_t *create_parms) { 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 = NULL; H5F_t *f = NULL; FUNC_ENTER(H5D_create, NULL); /* check args */ assert (loc); assert (name && *name); assert (type); assert (space); assert (create_parms); if (create_parms->pline.nfilters>0 && H5D_CHUNKED!=create_parms->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 is used, no filter support yet. */ if (IS_H5FD_MPIO(f) && create_parms->pline.nfilters>0) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel IO does not support filters yet"); } #endif /* Initialize the dataset object */ if (NULL==(new_dset = H5D_new(create_parms))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); } /* Copy datatype for dataset */ new_dset->type = H5T_copy(type, H5T_COPY_ALL); /* Mark any VL datatypes as being on disk now */ if (H5T_vlen_mark(new_dset->type, f, H5T_VLEN_DISK)<0) { HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "invalid VL location"); } efl = &(new_dset->create_parms->efl); /* Total raw data size */ new_dset->layout.type = new_dset->create_parms->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 (new_dset->create_parms->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; inew_dset->layout.dim[i]) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "only the first dimension can be extendible"); } } if (efl->nused>0) { hsize_t max_points = H5S_get_npoints_max (space); hsize_t max_storage = H5O_efl_total_size (efl); if (H5S_UNLIMITED==max_points) { if (H5O_EFL_UNLIMITED!=max_storage) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unlimited data space but finite storage"); } } else if (max_points * H5T_get_size (type) < max_points) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "data space * type size overflowed"); } else if (max_points * H5T_get_size (type) > max_storage) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "data space size exceeds external storage size"); } } else if (ndims>0 && max_dim[0]>new_dset->layout.dim[0]) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "extendible contiguous non-external dataset"); } break; case H5D_CHUNKED: /* * Chunked storage allows any type of data space extension, so we * don't even bother checking. */ if (new_dset->create_parms->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 (H5S_get_simple_extent_dims(space, NULL, max_dim)<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to query maximum dimensions"); } for (u=0; ulayout.ndims-1; u++) { if (max_dim[u]!=H5S_UNLIMITED && max_dim[u]create_parms->chunk_size[u]) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "chunk size must be <= maximum dimension size for fixed-sized dimensions"); } } /* Set the dataset's chunk sizes from the property list's chunk sizes */ for (u=0; ulayout.ndims-1; u++) { new_dset->layout.dim[u] = new_dset->create_parms->chunk_size[u]; } break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* 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"); } /* Convert the fill value to the dataset type and write the message */ if (H5O_fill_convert(&(new_dset->create_parms->fill), new_dset->type)<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to convert fill value to dataset type"); } if (new_dset->create_parms->fill.buf && H5O_modify(&(new_dset->ent), H5O_FILL, 0, H5O_FLAG_CONSTANT, &(new_dset->create_parms->fill))<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to update fill value header message"); } /* 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 (new_dset->create_parms->pline.nfilters>0 && H5O_modify (&(new_dset->ent), H5O_PLINE, 0, H5O_FLAG_CONSTANT, &(new_dset->create_parms->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"); } #ifdef QAK printf("%s: check 0.5\n",FUNC); #endif /* QAK */ /* 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. */ #ifdef QAK printf("%s: check 1.0\n",FUNC); #endif /* QAK */ if (0==efl->nused) { if (H5F_arr_create(f, &(new_dset->layout)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); } } else { new_dset->layout.addr = HADDR_UNDEF; } #ifdef QAK printf("%s: check 2.0\n",FUNC); #endif /* QAK */ /* Update layout message */ if (H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT, &(new_dset->layout)) < 0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "unable to update layout message"); } #ifdef QAK printf("%s: check 3.0\n",FUNC); #endif /* QAK */ /* Update external storage message */ if (efl->nused>0) { size_t heap_size = H5HL_ALIGN (1); for (i=0; inused; 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; inused; 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; } 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"); } } #ifdef QAK printf("%s: check 4.0\n",FUNC); #endif /* QAK */ /* Initialize the raw data */ if (H5D_init_storage(new_dset, space)<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize storage"); } #ifdef QAK printf("%s: check 6.0\n",FUNC); #endif /* QAK */ /* Success */ ret_value = new_dset; done: if (!ret_value && new_dset) { if (new_dset->type) H5T_close(new_dset->type); if (new_dset->create_parms) { H5P_close (new_dset->create_parms); new_dset->create_parms = NULL; } 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; FUNC_ENTER(H5D_isa, FAIL); assert(ent); /* Data type */ if ((exists=H5O_exists(ent, H5O_DTYPE, 0))<0) { HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read object header"); } else if (!exists) { HRETURN(FALSE); } /* Layout */ if ((exists=H5O_exists(ent, H5O_LAYOUT, 0))<0) { HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read object header"); } else if (!exists) { HRETURN(FALSE); } FUNC_LEAVE(TRUE); } /* *------------------------------------------------------------------------- * 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(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: * *------------------------------------------------------------------------- */ 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 */ unsigned u; FUNC_ENTER(H5D_open_oid, NULL); /* check args */ assert (ent); /* Allocate the dataset structure */ if (NULL==(dataset = H5D_new(NULL))) { 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 the optional fill value message */ if (NULL==H5O_read(&(dataset->ent), H5O_FILL, 0, &(dataset->create_parms->fill))) { H5E_clear(); HDmemset(&(dataset->create_parms->fill), 0, sizeof(dataset->create_parms->fill)); } /* Get the optional filters message */ if (NULL==H5O_read (&(dataset->ent), H5O_PLINE, 0, &(dataset->create_parms->pline))) { H5E_clear (); HDmemset (&(dataset->create_parms->pline), 0, sizeof(dataset->create_parms->pline)); } #ifdef H5_HAVE_PARALLEL /* If MPIO is used, no filter support yet. */ if (IS_H5FD_MPIO(dataset->ent.file) && dataset->create_parms->pline.nfilters>0) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel IO does not support filters yet"); } #endif /* * 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: dataset->create_parms->layout = H5D_CONTIGUOUS; 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. */ dataset->create_parms->layout = H5D_CHUNKED; dataset->create_parms->chunk_ndims = dataset->layout.ndims - 1; for (u = 0; u < dataset->layout.ndims - 1; u++) { dataset->create_parms->chunk_size[u] = dataset->layout.dim[u]; } break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* Get the external file list message, which might not exist */ if (NULL==H5O_read (&(dataset->ent), H5O_EFL, 0, &(dataset->create_parms->efl)) && !H5F_addr_defined (dataset->layout.addr)) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL, "storage address is undefined an no 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); } if (dataset->create_parms) { H5P_close (dataset->create_parms); } 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; FUNC_ENTER(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 || H5P_close(dataset->create_parms)); /* 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) { HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't free the type or creation property list, " "but the dataset was freed anyway."); } FUNC_LEAVE(SUCCEED); } /*------------------------------------------------------------------------- * 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. * *------------------------------------------------------------------------- */ 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*/) { hssize_t nelmts; /*number of elements */ 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; /*mem selection iteration info*/ H5S_sel_iter_t bkg_iter; /*background iteration info*/ H5S_sel_iter_t file_iter; /*file selection iter info*/ herr_t ret_value = FAIL; /*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 */ hbool_t must_convert; /*have to xfer the slow way*/ #ifdef H5_HAVE_PARALLEL H5FD_mpio_dxpl_t *dx = NULL; H5FD_mpio_xfer_t xfer_mode; /*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 #ifdef H5S_DEBUG H5_timer_t timer; #endif FUNC_ENTER(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==H5Pisa_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)); 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; } if (!mem_space) mem_space = file_space; nelmts = H5S_get_select_npoints(mem_space); #ifdef H5_HAVE_PARALLEL /* Collect Parallel I/O information for possible later use */ if (H5FD_MPIO==H5P_peek_hid_t(dxpl_id,H5D_XFER_VFL_ID_NAME)) { doing_mpio++; if (dx=H5P_peek_voidp(dxpl_id,H5D_XFER_VFL_INFO_NAME)) xfer_mode = dx->xfer_mode; else HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to retrieve data xfer info"); } /* Collective access is not permissible without the MPIO driver */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && !(IS_H5FD_MPIO(dataset->ent.file))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPIO driver only"); #endif #ifdef QAK printf("%s: check 1.0, nelmts=%d\n",FUNC,(int)nelmts); #endif /* QAK */ /* * 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 (nelmts!=H5S_get_select_npoints (file_space)) { HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); } 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"); } } if (NULL==(sconv=H5S_find(mem_space, file_space))) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space"); } #ifdef H5_HAVE_PARALLEL /* rky 980813 This is a temporary KLUGE. * The sconv functions should be set by H5S_find, * or we should use a different way to call the MPI-IO * mem-and-file-dataspace-xfer functions * (the latter in case the arguments to sconv_funcs * turn out to be inappropriate for MPI-IO). */ if (H5_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->read = H5S_mpio_spaces_read; } #endif /*H5_HAVE_PARALLEL*/ #ifdef QAK printf("%s: check 1.1, \n",FUNC); #endif /* QAK */ /* * If there is no type conversion then try reading directly into the * application's buffer. This saves at least one mem-to-mem copy. */ if (H5T_IS_NOOP(tpath) && sconv->read) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = (sconv->read)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->pline), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, mem_space, dxpl_id, buf/*out*/, &must_convert); if (status<0) { /* Supports only no conversion, type or space, for now. */ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed"); } if (must_convert) { /* sconv->read cannot do a direct transfer; * fall through and xfer the data in the more roundabout way */ } else { /* direct xfer accomplished successfully */ #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 goto succeed; } #ifdef H5D_DEBUG if (H5DEBUG(D)) { fprintf (H5DEBUG(D), "H5D: data space conversion could not be " "optimized for this case (using general method " "instead)\n"); } #endif H5E_clear (); } #ifdef QAK printf("%s: check 1.2, \n",FUNC); #endif /* QAK */ #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); } #endif } #endif /* * This is the general case. Figure out the strip mine size. */ if ((sconv->f->init)(file_space, &file_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); } if ((sconv->m->init)(mem_space, &mem_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); } if ((sconv->m->init)(mem_space, &bkg_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); } src_type_size = H5T_get_size(dataset->type); dst_type_size = H5T_get_size(mem_type); target_size = H5P_peek_size_t(dxpl_id,H5D_XFER_MAX_TEMP_BUF_NAME); #ifdef QAK printf("%s: check 2.0, src_type_size=%d, dst_type_size=%d, target_size=%d\n",FUNC,(int)src_type_size,(int)dst_type_size,(int)target_size); #endif /* QAK */ request_nelmts = target_size / MAX(src_type_size, dst_type_size); #ifdef QAK printf("%s: check 3.0, request_nelmts=%d\n",FUNC,(int)request_nelmts); #endif 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(H5Pget(dxpl_id, 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*/ } if (NULL==(tconv_buf=H5P_peek_voidp(dxpl_id,H5D_XFER_TCONV_BUF_NAME))) { #ifdef QAK printf("%s: check 3.1, allocating conversion buffer\n",FUNC); #endif /* 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"); } if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dxpl_id,H5D_XFER_BKGR_BUF_NAME))) { #ifdef QAK printf("%s: check 3.2, allocating conversion buffer\n",FUNC); #endif /* Allocate temporary buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,(size_t)(request_nelmts*dst_type_size),0))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } #ifdef QAK printf("%s: check 4.0, nelmts=%d, need_bkg=%d\n", FUNC,(int)nelmts,(int)need_bkg); #endif /* Start strip mining... */ H5_CHECK_OVERFLOW(nelmts,hssize_t,hsize_t); for (smine_start=0; smine_start<(hsize_t)nelmts; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ smine_nelmts = (sconv->f->avail)(file_space,&file_iter, MIN(request_nelmts, (nelmts-smine_start))); #ifdef QAK printf("%s: check 5.0, nelmts=%d, smine_start=%d, smine_nelmts=%d\n", FUNC,(int)nelmts,(int)smine_start,(int)smine_nelmts); #endif /* * 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 n = (sconv->f->gath)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->pline), &(dataset->create_parms->fill), &(dataset->create_parms->efl), 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"); } #ifdef QAK printf("%s: check 6.0\n",FUNC); #ifdef QAK { int i; int *b; /* if(qak_debug) { */ b=tconv_buf; printf("\ntconv_buf:"); for (i=0; im->gath)(buf, dst_type_size, mem_space, &bkg_iter, smine_nelmts, 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"); } } else if (need_bkg) { assert((request_nelmts*dst_type_size)==(hsize_t)((size_t)(request_nelmts*dst_type_size))); /*check for overflow*/ HDmemset(bkg_buf, 0, (size_t)(request_nelmts*dst_type_size)); } #ifdef QAK printf("%s: check 7.0\n",FUNC); #endif /* * 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"); } #ifdef QAK printf("%s: check 8.0\n",FUNC); #endif /* * Scatter the data into memory. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = (sconv->m->scat)(tconv_buf, dst_type_size, mem_space, &mem_iter, smine_nelmts, 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_IO, H5E_READERROR, FAIL, "scatter failed"); } #ifdef QAK printf("%s: check 9.0\n",FUNC); #endif /* QAK */ } succeed: ret_value = SUCCEED; 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); } #endif dx->xfer_mode = xfer_mode; } #endif /* Release selection iterators */ H5S_sel_iter_release(file_space,&file_iter); H5S_sel_iter_release(mem_space,&mem_iter); H5S_sel_iter_release(mem_space,&bkg_iter); if (src_id >= 0) H5I_dec_ref(src_id); if (dst_id >= 0) H5I_dec_ref(dst_id); if (tconv_buf && NULL==H5P_peek_voidp(dxpl_id,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dxpl_id,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(bkgr_conv,bkg_buf); if (free_this_space) H5S_close(free_this_space); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * 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. * *------------------------------------------------------------------------- */ 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) { hssize_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 = FAIL; /*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 */ hbool_t must_convert; /*have to xfer the slow way*/ #ifdef H5_HAVE_PARALLEL H5FD_mpio_dxpl_t *dx = NULL; H5FD_mpio_xfer_t xfer_mode; /*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 #ifdef H5S_DEBUG H5_timer_t timer; #endif FUNC_ENTER(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==H5Pisa_class(dxpl_id,H5P_DATASET_XFER)); #ifdef H5_HAVE_PARALLEL /* If MPIO 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) && H5T_get_class(mem_type)==H5T_VLEN) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet"); } #endif #ifdef H5_HAVE_PARALLEL /* If MPIO is used, no dataset region reference 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) && 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 VL datatypes yet"); } #endif /* 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)); #ifdef QAK printf("%s: check 0.3, buf=%p\n", FUNC,buf); #endif /* QAK */ 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; } if (!mem_space) mem_space = file_space; nelmts = H5S_get_select_npoints(mem_space); #ifdef H5_HAVE_PARALLEL /* Collect Parallel I/O information for possible later use */ if (H5FD_MPIO==H5P_peek_hid_t(dxpl_id,H5D_XFER_VFL_ID_NAME)) { doing_mpio++; if (dx=H5P_peek_voidp(dxpl_id,H5D_XFER_VFL_INFO_NAME)) xfer_mode = dx->xfer_mode; else HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to retrieve data xfer info"); } /* Collective access is not permissible without the MPIO driver */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && !(IS_H5FD_MPIO(dataset->ent.file))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPIO driver only"); #endif /* * 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. */ #ifdef QAK printf("%s: check 0.5, nelmts=%d, mem_space->rank=%d\n", FUNC, (int)nelmts, mem_space->extent.u.simple.rank); #endif /* QAK */ if (nelmts!=H5S_get_select_npoints (file_space)) { HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); } 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"); } } #ifdef QAK printf("%s: check 0.6, after H5T_find, tpath=%p, tpath->name=%s\n",FUNC,tpath,tpath->name); #endif /* QAK */ if (NULL==(sconv=H5S_find(mem_space, file_space))) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space"); } #ifdef H5_HAVE_PARALLEL /* rky 980813 This is a temporary KLUGE. * The sconv functions should be set by H5S_find, * or we should use a different way to call the MPI-IO * mem-and-file-dataspace-xfer functions * (the latter in case the arguments to sconv_funcs * turn out to be inappropriate for MPI-IO). */ if (H5_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->write = H5S_mpio_spaces_write; } #endif /*H5_HAVE_PARALLEL*/ /* * If there is no type conversion then try writing directly from * application buffer to file. */ #ifdef QAK printf("%s: check 0.7, H5T_IS_NOOP(path)=%d, sconv->write=%p\n", FUNC, (int)H5T_IS_NOOP(tpath), sconv->write); #endif /* QAK */ if (H5T_IS_NOOP(tpath) && sconv->write) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = (sconv->write)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->pline), &(dataset->create_parms->efl), H5T_get_size (dataset->type), file_space, mem_space, dxpl_id, buf, &must_convert/*out*/); if (status<0) { /* Supports only no conversion, type or space, for now. */ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed"); } if (must_convert) { /* sconv->write cannot do a direct transfer; * fall through and xfer the data in the more roundabout way */ } else { /* direct xfer accomplished successfully */ #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 goto succeed; } #ifdef H5D_DEBUG if (H5DEBUG(D)) { fprintf (H5DEBUG(D), "H5D: data space conversion could not be " "optimized for this case (using general method " "instead)\n"); } #endif H5E_clear (); } #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); } #endif } #endif /* * This is the general case. Figure out the strip mine size. */ if ((sconv->f->init)(file_space, &file_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); } if ((sconv->m->init)(mem_space, &mem_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); } if ((sconv->f->init)(file_space, &bkg_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); } src_type_size = H5T_get_size(mem_type); dst_type_size = H5T_get_size(dataset->type); target_size = H5P_peek_size_t(dxpl_id,H5D_XFER_MAX_TEMP_BUF_NAME); #ifdef QAK printf("%s: check 2.0, src_type_size=%d, dst_type_size=%d, target_size=%d\n",FUNC,(int)src_type_size,(int)dst_type_size,(int)target_size); #endif /* QAK */ request_nelmts = target_size / MAX (src_type_size, dst_type_size); #ifdef QAK printf("%s: check 3.0, request_nelmts=%d, tpath->cdata.need_bkg=%d\n",FUNC,(int)request_nelmts,(int)tpath->cdata.need_bkg); #endif 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(H5Pget(dxpl_id, 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*/ } if (NULL==(tconv_buf=H5P_peek_voidp(dxpl_id,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"); } if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dxpl_id,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate temporary buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,(size_t)(request_nelmts*dst_type_size),0))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } #ifdef QAK printf("%s: check 4.0, nelmts=%d, request_nelmts=%d, need_bkg=%d\n", FUNC,(int)nelmts,(int)request_nelmts,(int)need_bkg); #endif /* Start strip mining... */ H5_CHECK_OVERFLOW(nelmts,hssize_t,hsize_t); for (smine_start=0; smine_start<(hsize_t)nelmts; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ smine_nelmts = (sconv->f->avail)(file_space,&file_iter, MIN(request_nelmts, (nelmts-smine_start))); #ifdef QAK printf("%s: check 5.0, nelmts=%d, smine_start=%d, smine_nelmts=%d\n", FUNC,(int)nelmts,(int)smine_start,(int)smine_nelmts); #endif /* * 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 = (sconv->m->gath)(buf, src_type_size, mem_space, &mem_iter, smine_nelmts, 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"); } #ifdef QAK { int i; uint16_t *b; if(qak_debug) { b=tconv_buf; printf("\ntconv_buf:"); for (i=0; if->gath)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->pline), &(dataset->create_parms->fill), &(dataset->create_parms->efl), 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"); } } else if (need_bkg) { #ifdef QAK printf("%s: check 6.2, need_bkg=%d\n",FUNC,(int)need_bkg); #endif H5_CHECK_OVERFLOW(request_nelmts*dst_type_size,hsize_t,size_t); HDmemset(bkg_buf, 0, (size_t)(request_nelmts*dst_type_size)); } /* * 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"); } #ifdef QAK printf("%s: check 6.3\n",FUNC); #endif /* * Scatter the data out to the file. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = (sconv->f->scat)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->pline), &(dataset->create_parms->fill), &(dataset->create_parms->efl), dst_type_size, file_space, &file_iter, smine_nelmts, dxpl_id, tconv_buf); #ifdef QAK printf("%s: check 6.35\n",FUNC); #endif #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_DATASET, H5E_WRITEERROR, FAIL, "scatter failed"); } } #ifdef QAK printf("%s: check 6.4\n",FUNC); #endif /* * 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"); } succeed: ret_value = SUCCEED; 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); } #endif dx->xfer_mode = xfer_mode; } #endif /* Release selection iterators */ H5S_sel_iter_release(file_space,&file_iter); H5S_sel_iter_release(mem_space,&mem_iter); H5S_sel_iter_release(file_space,&bkg_iter); if (src_id >= 0) H5I_dec_ref(src_id); if (dst_id >= 0) H5I_dec_ref(dst_id); if (tconv_buf && NULL==H5P_peek_voidp(dxpl_id,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dxpl_id,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(bkgr_conv,bkg_buf); if (free_this_space) H5S_close(free_this_space); FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * 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: * *------------------------------------------------------------------------- */ herr_t H5D_extend (H5D_t *dataset, const hsize_t *size) { herr_t changed, ret_value=FAIL; H5S_t *space = NULL; FUNC_ENTER (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 (H5D_CONTIGUOUS==dataset->layout.type && dataset->create_parms->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"); } } ret_value = SUCCEED; 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) { return 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) { FUNC_ENTER (H5D_typeof, NULL); 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) { FUNC_ENTER (H5D_get_file, NULL); 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: * *------------------------------------------------------------------------- */ static herr_t H5D_init_storage(H5D_t *dset, const H5S_t *space) { hssize_t npoints, ptsperbuf; size_t bufsize=8*1024; size_t size; haddr_t addr; herr_t ret_value = FAIL; void *buf = NULL; FUNC_ENTER(H5D_init_storage, FAIL); assert(dset); assert(space); switch (dset->layout.type) { case H5D_CONTIGUOUS: /* * If the fill value is set then write it to the specified selection * even if it is all zero. This allows the application to force * filling when the underlying storage isn't initialized to zero. */ npoints = H5S_get_simple_extent_npoints(space); if (dset->create_parms->fill.buf && npoints==H5S_get_select_npoints(space)) { /* * 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 = (hssize_t)MAX(1, bufsize/dset->create_parms->fill.size); bufsize = ptsperbuf * dset->create_parms->fill.size; /* Allocate temporary buffer */ if ((buf=H5FL_BLK_ALLOC(fill_conv,bufsize,0))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer"); assert(ptsperbuf==(hssize_t)((size_t)ptsperbuf)); /*check for overflow*/ H5V_array_fill(buf, dset->create_parms->fill.buf, dset->create_parms->fill.size, (size_t)ptsperbuf); if (dset->create_parms->efl.nused) { addr = 0; } else { addr = dset->layout.addr; } while (npoints>0) { size = MIN(ptsperbuf, npoints) * dset->create_parms->fill.size; if (dset->create_parms->efl.nused) { if (H5O_efl_write(dset->ent.file, &(dset->create_parms->efl), addr, size, buf)<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); } } else { if (H5F_block_write(dset->ent.file, H5FD_MEM_DRAW, addr, size, H5P_DATASET_XFER_DEFAULT, buf)<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); } } npoints -= MIN(ptsperbuf, npoints); addr += size; } } else if (dset->create_parms->fill.buf) { /* * Fill the specified selection with the fill value. */ HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to initialize dataset with fill value"); } 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)) { /* 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, &(dset->create_parms->pline), &(dset->create_parms->fill))<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset"); } } #endif /*H5_HAVE_PARALLEL*/ break; } ret_value = SUCCEED; done: if (buf) H5FL_BLK_FREE(fill_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 size; FUNC_ENTER(H5Dget_storage_size, 0); H5TRACE1("h","i",dset_id); /* Check args */ if (H5I_DATASET!=H5I_get_type(dset_id) || NULL==(dset=H5I_object(dset_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset"); } size = H5D_get_storage_size(dset); FUNC_LEAVE(size); } /*------------------------------------------------------------------------- * 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) { hsize_t size; unsigned u; FUNC_ENTER(H5D_get_storage_size, 0); if (H5D_CHUNKED==dset->layout.type) { size = H5F_istore_allocated(dset->ent.file, dset->layout.ndims, dset->layout.addr); } else { for (u=0, size=1; ulayout.ndims; u++) { size *= dset->layout.dim[u]; } } FUNC_LEAVE(size); } /*------------------------------------------------------------------------- * 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=FAIL; FUNC_ENTER(H5Diterate, FAIL); H5TRACE5("e","xiixx",buf,type_id,space_id,op,operator_data); /* Check args */ if (NULL==op) HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid operator"); if (buf==NULL) HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer"); if (H5I_DATATYPE != H5I_get_type(type_id)) HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid datatype"); if (H5I_DATASPACE != H5I_get_type(space_id) || NULL == (space = H5I_object(space_id))) HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace"); ret_value=H5S_select_iterate(buf,type_id,space,op,operator_data); 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=FAIL; FUNC_ENTER(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) { HRETURN_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 (H5I_GENPROP_LST != H5I_get_type(plist_id) || TRUE!=H5Pisa_class(plist_id,H5P_DATASET_XFER)) HRETURN_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); 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(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=FAIL; FUNC_ENTER(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"); /* Set the correct return value, if we get this far */ ret_value=0; 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() */ herr_t ret_value=FAIL; FUNC_ENTER(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) { HRETURN_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"); /* Change to the custom memory allocation routines for reading VL data */ if((vlen_bufsize.xfer_pid=H5Pcreate_list(H5P_DATASET_XFER))<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTCREATE, FAIL, "no dataset xfer plists available"); if(H5Pset_vlen_mem_manager(vlen_bufsize.xfer_pid,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) H5Pclose_list(vlen_bufsize.xfer_pid); FUNC_LEAVE(ret_value); } /* end H5Dvlen_get_buf_size() */ /*------------------------------------------------------------------------- * 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; FUNC_ENTER(H5Ddebug, FAIL); H5TRACE2("e","iIu",dset_id,flags); /* Check args */ if (H5I_DATASET!=H5I_get_type(dset_id) || NULL==(dset=H5I_object(dset_id))) { HRETURN_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); } FUNC_LEAVE(SUCCEED); }