/**************************************************************************** * 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. * * * ****************************************************************************/ #ifdef RCSID static char RcsId[] = "@(#)$Revision$"; #endif /* $Id$ */ #include /* Generic Functions */ #include /* IDs */ #include /* Cache */ #include /* Dataset functions */ #include /* Error handling */ #include /* Group headers */ #include /* Name heap */ #include /* File space allocation header */ #include /* Memory management */ #include /* Object headers */ #include /* Property lists */ #include /* Dataspace functions rky 980813 */ #include /* Data filters */ #ifdef QAK int qak_debug=0; #endif /* QAK */ #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. */ /* External file list */ {H5F_ADDR_UNDEF, /* External file list heap address */ 0, /*...slots allocated */ 0, /*...slots used */ NULL}, /*...slot array */ /* Filters */ {0, 0, NULL} /* No filters in pipeline */ }; /* Default dataset transfer property list */ const H5D_xfer_t H5D_xfer_dflt = { 1024*1024, /* Temporary buffer size */ NULL, /* Type conversion buffer or NULL */ NULL, /* Background buffer or NULL */ H5T_BKG_NO, /* Type of background buffer needed */ #ifdef HAVE_PARALLEL H5D_XFER_DFLT, /* Independent data transfer */ #endif }; /* Interface initialization? */ static hbool_t interface_initialize_g = FALSE; #define INTERFACE_INIT H5D_init_interface static herr_t H5D_init_interface(void); static void H5D_term_interface(void); #ifdef HAVE_PARALLEL static herr_t H5D_allocate (H5D_t *dataset); #endif /*-------------------------------------------------------------------------- NAME H5D_init_interface -- Initialize interface-specific information USAGE herr_t H5D_init_interface() RETURNS SUCCEED/FAIL DESCRIPTION Initializes any interface-specific data or routines. --------------------------------------------------------------------------*/ static herr_t H5D_init_interface(void) { herr_t ret_value = SUCCEED; FUNC_ENTER(H5D_init_interface, FAIL); /* Initialize the atom group for the dataset IDs */ if ((ret_value = H5I_init_group(H5_DATASET, H5I_DATASETID_HASHSIZE, H5D_RESERVED_ATOMS, (herr_t (*)(void *)) H5D_close)) != FAIL) { ret_value = H5_add_exit(H5D_term_interface); } FUNC_LEAVE(ret_value); } /*-------------------------------------------------------------------------- NAME H5D_term_interface PURPOSE Terminate various H5D objects USAGE void H5D_term_interface() RETURNS SUCCEED/FAIL DESCRIPTION Release the atom group and any other resources allocated. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS Can't report errors... EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ static void H5D_term_interface(void) { H5I_destroy_group(H5_DATASET); } /*------------------------------------------------------------------------- * 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 (H5_DATATYPE != H5I_group(type_id) || NULL == (type = H5I_object(type_id))) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a type"); } if (H5_DATASPACE != H5I_group(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(H5_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(H5_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: Success: SUCCEED * * Failure: FAIL * * 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 (H5_DATASET != H5I_group(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 (H5_DATASET!=H5I_group (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 (H5_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 (H5_DATASET!=H5I_group (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"); } 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 (H5_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 (H5_DATASET!=H5I_group (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"); } /* Create an atom */ if ((ret_value=H5I_register ((H5I_group_t)(H5_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: Success: SUCCEED * * Failure: FAIL * * 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; const H5D_xfer_t *xfer_parms = 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 (H5_DATASET != H5I_group(dset_id) || NULL == (dset = H5I_object(dset_id)) || NULL == dset->ent.file) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } if (H5_DATATYPE != H5I_group(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 (H5_DATASPACE != H5I_group(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 (H5_DATASPACE != H5I_group(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"); } } if (H5P_DEFAULT == plist_id) { xfer_parms = &H5D_xfer_dflt; } else if (H5P_DATASET_XFER != H5P_get_class(plist_id) || NULL == (xfer_parms = H5I_object(plist_id))) { 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, xfer_parms, 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: Success: SUCCEED * * Failure: FAIL * * 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; const H5D_xfer_t *xfer_parms = 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 (H5_DATASET != H5I_group(dset_id) || NULL == (dset = H5I_object(dset_id)) || NULL == dset->ent.file) { HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); } if (H5_DATATYPE != H5I_group(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 (H5_DATASPACE != H5I_group(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 (H5_DATASPACE != H5I_group(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"); } } if (H5P_DEFAULT == plist_id) { xfer_parms = &H5D_xfer_dflt; } else if (H5P_DATASET_XFER != H5P_get_class(plist_id) || NULL == (xfer_parms = H5I_object(plist_id))) { 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, xfer_parms, 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: Success: SUCCEED * * Failure: FAIL * * 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 (H5_DATASET!=H5I_group (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_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. * *------------------------------------------------------------------------- */ 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; intn i, ndims; hsize_t max_dim[H5O_LAYOUT_NDIMS]; H5O_efl_t *efl = NULL; H5F_t *f = loc->file; FUNC_ENTER(H5D_create, NULL); /* check args */ assert (f); assert (loc); assert (name && *name); assert (type); assert (space); assert (create_parms); #ifdef HAVE_PARALLEL /* If MPIO is used, no filter support yet. */ if (f->shared->access_parms->driver == H5F_LOW_MPIO && create_parms->pline.nfilters>0) { HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL, "Parallel IO does not support filters yet"); } #endif 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"); } /* Initialize the dataset object */ if (NULL==(new_dset = H5MM_calloc(sizeof(H5D_t)))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); } H5F_addr_undef(&(new_dset->ent.header)); new_dset->type = H5T_copy(type, H5T_COPY_ALL); new_dset->create_parms = H5P_copy (H5P_DATASET_CREATE, create_parms); 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(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"); } for (i=0; ilayout.ndims-1; i++) { new_dset->layout.dim[i] = new_dset->create_parms->chunk_size[i]; } break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet"); } /* Create (open for write access) an object header */ if (H5O_create(f, 96, &(new_dset->ent)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to create dataset object header"); } /* 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"); } /* * Initialize storage. We assume that external storage is already * initialized by the caller, or at least will be before I/O is * performed. */ 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 { H5F_addr_undef (&(new_dset->layout.addr)); } /* 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"); } /* 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))<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"); } 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"); } } /* 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"); } #ifdef HAVE_PARALLEL /* * If the dataset uses chunk storage and is accessed via * parallel I/O, allocate file space for all chunks now. */ if (new_dset->ent.file->shared->access_parms->driver == H5F_LOW_MPIO && new_dset->layout.type == H5D_CHUNKED){ if (H5D_allocate(new_dset)==FAIL){ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "fail in file space allocation for chunks"); } } #endif /* HAVE_PARALLEL */ /* 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 (H5P_DATASET_CREATE, 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; H5MM_xfree(new_dset); } FUNC_LEAVE(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_open * * Purpose: Finds a dataset named NAME in file F and builds a descriptor * for it, opening it for access. * * Return: Success: Pointer to a new dataset descriptor. * * Failure: NULL * * Errors: * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space message is no longer cached in the dataset struct. * *------------------------------------------------------------------------- */ 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 */ intn i; H5S_t *space = NULL; FUNC_ENTER(H5D_open, NULL); /* check args */ assert (loc); assert (name && *name); if (NULL==(dataset = H5MM_calloc(sizeof(H5D_t)))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); } dataset->create_parms = H5P_copy (H5P_DATASET_CREATE, &H5D_create_dflt); H5F_addr_undef(&(dataset->ent.header)); /* Open the dataset object */ if (H5G_find(loc, name, NULL, &(dataset->ent)) < 0) { HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found"); } 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 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 HAVE_PARALLEL /* If MPIO is used, no filter support yet. */ if (dataset->ent.file->shared->access_parms->driver == H5F_LOW_MPIO && 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 (i = 0; i < dataset->layout.ndims - 1; i++) { dataset->create_parms->chunk_size[i] = dataset->layout.dim[i]; } 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"); } #ifdef HAVE_PARALLEL /* * If the dataset uses chunk storage and is accessed via * parallel I/O, and file is open writable, * allocate file space for chunks that have not been * allocated in its "previous access". */ if (dataset->ent.file->shared->access_parms->driver==H5F_LOW_MPIO && dataset->layout.type == H5D_CHUNKED && (dataset->ent.file->intent & H5F_ACC_RDWR)){ if (H5D_allocate(dataset)==FAIL){ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "fail in file space allocation dataset"); } } #endif /* HAVE_PARALLEL */ /* Success */ ret_value = dataset; done: if (space) H5S_close (space); if (!ret_value && 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 (H5P_DATASET_CREATE, dataset->create_parms); } dataset->ent.file = NULL; H5MM_xfree(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: Success: SUCCEED * * Failure: FAIL * * 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) { uintn 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 (H5P_DATASET_CREATE, 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; H5MM_xfree(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: Success: SUCCEED * * Failure: FAIL * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space is no longer cached in the dataset struct. * * Robb Matzke, 11 Aug 1998 * Added timing calls around all the data space I/O functions. * * rky 980918 * Added must_convert to do non-optimized read when necessary. * *------------------------------------------------------------------------- */ herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, const H5D_xfer_t *xfer_parms, void *buf/*out*/) { hsize_t nelmts; /*number of elements */ size_t smine_start; /*strip mine start loc */ size_t n, smine_nelmts; /*elements per strip */ uint8 *tconv_buf = NULL; /*data type conv buffer */ uint8 *bkg_buf = NULL; /*background buffer */ H5T_conv_t tconv_func = NULL; /*conversion function */ 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*/ H5T_cdata_t *cdata = NULL; /*type conversion data */ herr_t ret_value = FAIL; herr_t 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 */ size_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 H5T_DEBUG H5_timer_t timer; #endif FUNC_ENTER(H5D_read, FAIL); /* check args */ assert(dataset && dataset->ent.file); assert(mem_type); assert(xfer_parms); assert(buf); /* Initialize these before any errors can occur */ HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t)); HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t)); HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t)); 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 HAVE_PARALLEL /* * Check if collective data transfer requested. */ if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){ /* * Verify that the file can support collective access. The check may * not be necessarily since collective access can always be simulated * by independent access. Nevertheless, must check driver is MPIO * before using those access_mode which exists only for MPIO case. */ if (dataset->ent.file->shared->access_parms->driver != H5F_LOW_MPIO) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access not permissible"); } #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. */ 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 == (tconv_func = H5T_find(dataset->type, mem_type, xfer_parms->need_bkg, &cdata))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } else if (H5T_conv_noop!=tconv_func) { if ((src_id=H5I_register(H5_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0 || (dst_id=H5I_register(H5_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 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 && H5F_LOW_MPIO==dataset->ent.file->shared->access_parms->driver) { sconv->read = H5S_mpio_spaces_read; } #endif /*HAVE_PARALLEL*/ /* * 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_conv_noop==tconv_func && sconv->read) { 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, xfer_parms->xfer_mode, 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 */ 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 (); } /* * This is the general case. Figure out the strip mine size. */ src_type_size = H5T_get_size(dataset->type); dst_type_size = H5T_get_size(mem_type); target_size = xfer_parms->buf_size; request_nelmts = target_size / MAX(src_type_size, dst_type_size); if (request_nelmts<=0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); } if ((sconv->f->init)(&(dataset->layout), file_space, &file_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); } if ((sconv->m->init)(&(dataset->layout), mem_space, &mem_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); } if ((sconv->m->init)(&(dataset->layout), mem_space, &bkg_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); } #ifdef QAK printf("%s: check 3.0, request_nelmts=%d\n",FUNC,(int)request_nelmts); #endif /* * 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 (cdata->need_bkg) { need_bkg = MAX (cdata->need_bkg, xfer_parms->need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } if (NULL==(tconv_buf=xfer_parms->tconv_buf)) { if (NULL==(tconv_buf = H5MM_malloc (target_size))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } } if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) { if (NULL==(bkg_buf = H5MM_malloc (request_nelmts * dst_type_size))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background buffer"); } } #ifdef QAK printf("%s: check 4.0, nelmts=%d, need_bkg=%d\n", FUNC,(int)nelmts,(int)need_bkg); #endif /* Start strip mining... */ for (smine_start=0; smine_startf->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->efl), src_type_size, file_space, &file_iter, smine_nelmts, xfer_parms->xfer_mode, 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); printf("%s: check 6.5\n",FUNC); { int i; uint16 *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"); } } #ifdef QAK printf("%s: check 7.0\n",FUNC); #endif /* * Perform data type conversion. */ #ifdef H5T_DEBUG H5T_timer_begin (&timer, cdata); #endif cdata->command = H5T_CONV_CONV; status = (tconv_func)(src_id, dst_id, cdata, smine_nelmts, tconv_buf, bkg_buf); #ifdef H5T_DEBUG H5T_timer_end (&timer, cdata, smine_nelmts); #endif if (status<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: /* 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==xfer_parms->tconv_buf) H5MM_xfree(tconv_buf); if (bkg_buf && NULL==xfer_parms->bkg_buf) H5MM_xfree (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: Success: SUCCEED * * Failure: FAIL * * 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. * *------------------------------------------------------------------------- */ herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, const H5D_xfer_t *xfer_parms, const void *buf) { hsize_t nelmts; /*total number of elmts */ size_t smine_start; /*strip mine start loc */ size_t n, smine_nelmts; /*elements per strip */ uint8 *tconv_buf = NULL; /*data type conv buffer */ uint8 *bkg_buf = NULL; /*background buffer */ H5T_conv_t tconv_func = NULL; /*conversion function */ 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*/ H5T_cdata_t *cdata = NULL; /*type conversion data */ herr_t ret_value = FAIL, 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 */ size_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 H5T_DEBUG H5_timer_t timer; #endif FUNC_ENTER(H5D_write, FAIL); /* check args */ assert(dataset && dataset->ent.file); assert(mem_type); assert(xfer_parms); assert(buf); /* Initialize these before any errors can occur */ HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t)); HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t)); HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t)); if (0==(dataset->ent.file->intent & 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 HAVE_PARALLEL /* * Check if collective data transfer requested. */ if (xfer_parms->xfer_mode == H5D_XFER_COLLECTIVE){ /* * Verify that the file can support collective access. The check may * not be necessarily since collective access can always be simulated * by independent access. Nevertheless, must check driver is MPIO * before using those access_mode which exists only for MPIO case. */ if (dataset->ent.file->shared->access_parms->driver != H5F_LOW_MPIO) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access not permissible"); } #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 == (tconv_func = H5T_find(mem_type, dataset->type, xfer_parms->need_bkg, &cdata))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } else if (H5T_conv_noop!=tconv_func) { if ((src_id = H5I_register(H5_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0 || (dst_id = H5I_register(H5_DATATYPE, H5T_copy(dataset->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 memory to file data space"); } #ifdef 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 && H5F_LOW_MPIO==dataset->ent.file->shared->access_parms->driver) { sconv->write = H5S_mpio_spaces_write; } #endif /*HAVE_PARALLEL*/ /* * If there is no type conversion then try writing directly from * application buffer to file. */ if (H5T_conv_noop==tconv_func && sconv->write) { 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, xfer_parms->xfer_mode, buf, &must_convert /*out*/ ); if (status<0) { /* Supports only no conversion, type or space, for now. */ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, 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 */ 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 (); } /* * This is the general case. Figure out the strip mine size. */ src_type_size = H5T_get_size(mem_type); dst_type_size = H5T_get_size(dataset->type); target_size = xfer_parms->buf_size; request_nelmts = target_size / MAX (src_type_size, dst_type_size); if (request_nelmts<=0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); } if ((sconv->f->init)(&(dataset->layout), file_space, &file_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); } if ((sconv->m->init)(&(dataset->layout), mem_space, &mem_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); } if ((sconv->f->init)(&(dataset->layout), file_space, &bkg_iter)<0) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); } #ifdef QAK printf("%s: check 3.0, request_nelmts=%d\n",FUNC,(int)request_nelmts); #endif /* * 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 (cdata->need_bkg) { need_bkg = MAX (cdata->need_bkg, xfer_parms->need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } if (NULL==(tconv_buf=xfer_parms->tconv_buf)) { if (NULL==(tconv_buf = H5MM_malloc (target_size))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } } if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) { if (NULL==(bkg_buf = H5MM_malloc (request_nelmts * dst_type_size))) { HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background buffer"); } } #ifdef QAK printf("%s: check 4.0, nelmts=%d, need_bkg=%d\n", FUNC,(int)nelmts,(int)need_bkg); #endif /* Start strip mining... */ for (smine_start=0; smine_startf->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 *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->efl), dst_type_size, file_space, &bkg_iter, smine_nelmts, xfer_parms->xfer_mode, 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"); } } /* * Perform data type conversion. */ #ifdef H5T_DEBUG H5T_timer_begin (&timer, cdata); #endif cdata->command = H5T_CONV_CONV; status = (tconv_func) (src_id, dst_id, cdata, smine_nelmts, tconv_buf, bkg_buf); #ifdef H5T_DEBUG H5T_timer_end (&timer, cdata, smine_nelmts); #endif if (status<0) { HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); } /* * Scatter the data out to the file. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = (sconv->f->scat)(dataset->ent.file, &(dataset->layout), &(dataset->create_parms->pline), &(dataset->create_parms->efl), dst_type_size, file_space, &file_iter, smine_nelmts, xfer_parms->xfer_mode, tconv_buf); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].scat_timer), &timer); sconv->stats[0].scat_nbytes += smine_nelmts * dst_type_size; sconv->stats[0].scat_ncalls++; #endif if (status<0) { HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed"); } } /* * 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: /* 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==xfer_parms->tconv_buf) H5MM_xfree(tconv_buf); if (bkg_buf && NULL==xfer_parms->bkg_buf) H5MM_xfree (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: Success: SUCCEED * * Failure: FAIL * * 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"); } /* Save the new dataspace in the file if necessary */ if (changed>0){ if (H5S_modify (&(dataset->ent), space)<0) { HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace"); } #ifdef HAVE_PARALLEL /* * If the dataset uses chunk storage and is accessed via * parallel I/O, need to allocate file space for all extended * chunks now. */ if (dataset->ent.file->shared->access_parms->driver==H5F_LOW_MPIO && dataset->layout.type==H5D_CHUNKED){ if (H5D_allocate(dataset)==FAIL){ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "fail in file space allocation for chunks"); } } #endif /* HAVE_PARALLEL */ } 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); } #ifdef HAVE_PARALLEL /*------------------------------------------------------------------------- * Function: H5D_allocate * * Purpose: Allocate file space for the data storage of the dataset. * Return SUCCEED if all needed allocation succeed, otherwise * FAIL. * * Return: Success: SUCCEED * * Failure: FAIL * * Note: Current implementation allocates chunked dataset only. * * Programmer: Albert Cheng * July 9, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_allocate (H5D_t *dataset) { H5S_t *space = NULL; herr_t ret_value = FAIL; hsize_t space_dim[H5O_LAYOUT_NDIMS]; intn space_ndims; H5O_layout_t *layout; FUNC_ENTER(H5D_allocate, FAIL); #ifdef AKC printf("Enter %s:\n", FUNC); #endif /* Check args */ assert(dataset); assert(&(dataset->layout)); layout = &(dataset->layout); assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS); assert(H5F_addr_defined(&(layout->addr))); switch (layout->type) { case H5D_CONTIGUOUS: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet"); case H5D_CHUNKED: if (NULL==(space=H5S_read (&(dataset->ent)))) { HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data space info from dataset header"); } /* get current dims of dataset */ if ((space_ndims=H5S_get_simple_extent_dims(space, space_dim, NULL)) <= 0 || space_ndims+1 != layout->ndims){ HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate chunk storage"); } /* copy the element size over */ space_dim[space_ndims] = layout->dim[space_ndims]; if (H5F_istore_allocate(dataset->ent.file, (layout), space_dim, &(dataset->create_parms->pline))==FAIL){ HRETURN(FAIL); } break; default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "not implemented yet"); } ret_value = SUCCEED; done: if (space) H5S_close(space); FUNC_LEAVE(ret_value); } #endif