diff options
Diffstat (limited to 'src/H5D.c')
| -rw-r--r-- | src/H5D.c | 181 |
1 files changed, 111 insertions, 70 deletions
@@ -5,12 +5,10 @@ * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /****************/ @@ -24,6 +22,7 @@ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ +#include "H5CXprivate.h" /* API Contexts */ #include "H5Dpkg.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free lists */ @@ -109,7 +108,6 @@ H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, H5G_loc_t loc; /* Object location to insert dataset into */ H5D_t *dset = NULL; /* New dataset's info */ const H5S_t *space; /* Dataspace for dataset */ - hid_t dxpl_id = H5AC_ind_read_dxpl_id; /* dxpl used by library */ hid_t ret_value; /* Return value */ FUNC_ENTER_API(FAIL) @@ -138,12 +136,12 @@ H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, if(TRUE != H5P_isa_class(dcpl_id, H5P_DATASET_CREATE)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not dataset create property list ID") - /* Verify access property list and get correct dxpl */ - if(H5P_verify_apl_and_dxpl(&dapl_id, H5P_CLS_DACC, &dxpl_id, loc_id, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set access and transfer property lists") + /* Verify access property list and set up collective metadata if appropriate */ + if(H5CX_set_apl(&dapl_id, H5P_CLS_DACC, loc_id, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info") /* Create the new dataset & get its ID */ - if(NULL == (dset = H5D__create_named(&loc, name, type_id, space, lcpl_id, dcpl_id, dapl_id, dxpl_id))) + if(NULL == (dset = H5D__create_named(&loc, name, type_id, space, lcpl_id, dcpl_id, dapl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset") if((ret_value = H5I_register(H5I_DATASET, dset, TRUE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataset") @@ -199,7 +197,6 @@ H5Dcreate_anon(hid_t loc_id, hid_t type_id, hid_t space_id, hid_t dcpl_id, H5G_loc_t loc; /* Object location to insert dataset into */ H5D_t *dset = NULL; /* New dataset's info */ const H5S_t *space; /* Dataspace for dataset */ - hid_t dxpl_id = H5AC_ind_read_dxpl_id; /* dxpl used by library */ hid_t ret_value; /* Return value */ FUNC_ENTER_API(FAIL) @@ -218,12 +215,12 @@ H5Dcreate_anon(hid_t loc_id, hid_t type_id, hid_t space_id, hid_t dcpl_id, if(TRUE != H5P_isa_class(dcpl_id, H5P_DATASET_CREATE)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not dataset create property list ID") - /* Verify access property list and get correct dxpl */ - if(H5P_verify_apl_and_dxpl(&dapl_id, H5P_CLS_DACC, &dxpl_id, loc_id, TRUE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set access and transfer property lists") + /* Verify access property list and set up collective metadata if appropriate */ + if(H5CX_set_apl(&dapl_id, H5P_CLS_DACC, loc_id, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info") /* build and open the new dataset */ - if(NULL == (dset = H5D__create(loc.oloc->file, type_id, space, dcpl_id, dapl_id, dxpl_id))) + if(NULL == (dset = H5D__create_anon(loc.oloc->file, type_id, space, dcpl_id, dapl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create dataset") /* Register the new dataset to get an ID for it */ @@ -240,7 +237,7 @@ done: HDONE_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get object location of dataset") /* Decrement refcount on dataset's object header in memory */ - if(H5O_dec_rc_by_loc(oloc, dxpl_id) < 0) + if(H5O_dec_rc_by_loc(oloc) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to decrement refcount on newly created object") } /* end if */ @@ -275,7 +272,6 @@ H5Dopen2(hid_t loc_id, const char *name, hid_t dapl_id) { H5D_t *dset = NULL; H5G_loc_t loc; /* Object location of group */ - hid_t dxpl_id = H5AC_ind_read_dxpl_id; /* dxpl to use to open datset */ hid_t ret_value; FUNC_ENTER_API(FAIL) @@ -287,12 +283,12 @@ H5Dopen2(hid_t loc_id, const char *name, hid_t dapl_id) if(!name || !*name) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name") - /* Verify access property list and get correct dxpl */ - if(H5P_verify_apl_and_dxpl(&dapl_id, H5P_CLS_DACC, &dxpl_id, loc_id, FALSE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set access and transfer property lists") + /* Verify access property list and set up collective metadata if appropriate */ + if(H5CX_set_apl(&dapl_id, H5P_CLS_DACC, loc_id, FALSE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info") /* Open the dataset */ - if(NULL == (dset = H5D__open_name(&loc, name, dapl_id, dxpl_id))) + if(NULL == (dset = H5D__open_name(&loc, name, dapl_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open dataset") /* Register an atom for the dataset */ @@ -303,6 +299,7 @@ done: if(ret_value < 0) if(dset && H5D_close(dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataset") + FUNC_LEAVE_API(ret_value) } /* end H5Dopen2() */ @@ -367,15 +364,15 @@ H5Dget_space(hid_t dset_id) H5D_t *dset = NULL; hid_t ret_value; - FUNC_ENTER_API(FAIL) + FUNC_ENTER_API(H5I_INVALID_HID) H5TRACE1("i", "i", dset_id); /* Check args */ if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, H5I_INVALID_HID, "not a dataset") - if((ret_value = H5D_get_space(dset)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get dataspace") + if((ret_value = H5D__get_space(dset)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5I_INVALID_HID, "unable to get dataspace") done: FUNC_LEAVE_API(ret_value) @@ -410,7 +407,7 @@ H5Dget_space_status(hid_t dset_id, H5D_space_status_t *allocation) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") /* Read dataspace address and return */ - if(H5D__get_space_status(dset, allocation, H5AC_ind_read_dxpl_id) < 0) + if(H5D__get_space_status(dset, allocation) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get space status") done: @@ -437,7 +434,6 @@ done: hid_t H5Dget_type(hid_t dset_id) { - H5D_t *dset; /* Dataset */ hid_t ret_value; /* Return value */ @@ -448,7 +444,7 @@ H5Dget_type(hid_t dset_id) if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") - if((ret_value = H5D_get_type(dset)) < 0) + if((ret_value = H5D__get_type(dset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to get dataspace") done: @@ -475,18 +471,18 @@ done: hid_t H5Dget_create_plist(hid_t dset_id) { - H5D_t *dataset; /* Dataset structure */ - hid_t ret_value = SUCCEED; /* Return value */ + H5D_t *dataset; /* Dataset structure */ + hid_t ret_value; /* Return value */ - FUNC_ENTER_API(FAIL) + FUNC_ENTER_API(H5I_INVALID_HID) H5TRACE1("i", "i", dset_id); /* Check args */ if(NULL == (dataset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, H5I_INVALID_HID, "not a dataset") - if((ret_value = H5D_get_create_plist(dataset)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't get creation plist") + if((ret_value = H5D__get_create_plist(dataset)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, H5I_INVALID_HID, "Can't get creation plist") done: FUNC_LEAVE_API(ret_value) @@ -579,7 +575,7 @@ H5Dget_storage_size(hid_t dset_id) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataset") /* Set return value */ - if(H5D__get_storage_size(dset, H5AC_ind_read_dxpl_id, &ret_value) < 0) + if(H5D__get_storage_size(dset, &ret_value) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't get size of dataset's storage") done: @@ -734,13 +730,13 @@ done: *------------------------------------------------------------------------- */ herr_t -H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf) +H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t dxpl_id, void *buf) { H5S_t *space; /* Dataspace for iteration */ herr_t ret_value; /* Return value */ FUNC_ENTER_API(FAIL) - H5TRACE4("e", "iii*x", type_id, space_id, plist_id, buf); + H5TRACE4("e", "iii*x", type_id, space_id, dxpl_id, buf); /* Check args */ if(H5I_DATATYPE != H5I_get_type(type_id) || buf == NULL) @@ -751,14 +747,17 @@ H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspace does not have extent set") /* 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(H5P_DEFAULT == dxpl_id) + dxpl_id = H5P_DATASET_XFER_DEFAULT; else - if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_XFER)) + if(TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") + /* Set DXPL for operation */ + H5CX_set_dxpl(dxpl_id); + /* Call internal routine */ - ret_value = H5D_vlen_reclaim(type_id, space, plist_id, buf); + ret_value = H5D_vlen_reclaim(type_id, space, buf); done: FUNC_LEAVE_API(ret_value) @@ -793,13 +792,12 @@ herr_t H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id, hsize_t *size) { - H5D_vlen_bufsize_t vlen_bufsize = {0, 0, 0, 0, 0, 0, 0}; + H5D_vlen_bufsize_t vlen_bufsize = {0, 0, 0, 0, 0, 0}; H5D_t *dset; /* Dataset for operation */ H5S_t *fspace = NULL; /* Dataset's dataspace */ H5S_t *mspace = NULL; /* Memory dataspace */ char bogus; /* bogus value to pass to H5Diterate() */ H5S_t *space; /* Dataspace for iteration */ - H5P_genplist_t *plist; /* Property list */ H5T_t *type; /* Datatype */ H5S_sel_iter_op_t dset_op; /* Operator for iteration */ herr_t ret_value; /* Return value */ @@ -839,17 +837,9 @@ H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id, if(NULL == (vlen_bufsize.vl_tbuf = H5FL_BLK_MALLOC(vlen_vl_buf, (size_t)1))) 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 = H5P_create_id(H5P_CLS_DATASET_XFER_g, FALSE)) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTCREATE, FAIL, "no dataset xfer plists available") - - /* Get the property list struct */ - if(NULL == (plist = (H5P_genplist_t *)H5I_object(vlen_bufsize.xfer_pid))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") - /* Set the memory manager to the special allocation routine */ - if(H5P_set_vlen_mem_manager(plist, H5D__vlen_get_buf_size_alloc, &vlen_bufsize, NULL, NULL) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't set VL data allocation routine") + if(H5CX_set_vlen_alloc_info(H5D__vlen_get_buf_size_alloc, &vlen_bufsize, NULL, NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set VL data allocation routine") /* Set the initial number of bytes required */ vlen_bufsize.size = 0; @@ -874,8 +864,6 @@ done: vlen_bufsize.fl_tbuf = H5FL_BLK_FREE(vlen_fl_buf, vlen_bufsize.fl_tbuf); if(vlen_bufsize.vl_tbuf != NULL) vlen_bufsize.vl_tbuf = H5FL_BLK_FREE(vlen_vl_buf, vlen_bufsize.vl_tbuf); - if(vlen_bufsize.xfer_pid > 0 && H5I_dec_ref(vlen_bufsize.xfer_pid) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to decrement ref count on property list") FUNC_LEAVE_API(ret_value) } /* end H5Dvlen_get_buf_size() */ @@ -909,12 +897,16 @@ H5Dset_extent(hid_t dset_id, const hsize_t size[]) if(!size) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified") + /* Set up collective metadata if appropriate */ + if(H5CX_set_loc(dset_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set collective metadata read info") + /* Private function */ - if(H5D__set_extent(dset, size, H5AC_ind_read_dxpl_id) < 0) + if(H5D__set_extent(dset, size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set extend dataset") done: - FUNC_LEAVE_API(ret_value) + FUNC_LEAVE_API(ret_value) } /* end H5Dset_extent() */ @@ -933,7 +925,7 @@ done: herr_t H5Dflush(hid_t dset_id) { - H5D_t *dset; /* Dataset for this operation */ + H5D_t *dset; /* Dataset for this operation */ herr_t ret_value = SUCCEED; /* return value */ FUNC_ENTER_API(FAIL) @@ -943,13 +935,13 @@ H5Dflush(hid_t dset_id) if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") - /* Flush any dataset information still cached in memory */ - if(H5D__flush_real(dset, H5AC_ind_read_dxpl_id) < 0) - HDONE_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to flush cached dataset info") + /* Set up collective metadata if appropriate */ + if(H5CX_set_loc(dset_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set collective metadata read info") - /* Flush object's metadata to file */ - if(H5O_flush_common(&dset->oloc, dset_id, H5AC_ind_read_dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush dataset and object flush callback") + /* Flush dataset information cached in memory */ + if(H5D__flush(dset, dset_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush cached dataset info") done: FUNC_LEAVE_API(ret_value) @@ -971,8 +963,8 @@ done: herr_t H5Drefresh(hid_t dset_id) { - H5D_t *dset; /* Dataset to refresh */ - herr_t ret_value = SUCCEED; /* return value */ + H5D_t *dset; /* Dataset to refresh */ + herr_t ret_value = SUCCEED; /* return value */ FUNC_ENTER_API(FAIL) H5TRACE1("e", "i", dset_id); @@ -981,8 +973,12 @@ H5Drefresh(hid_t dset_id) if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + /* Set up collective metadata if appropriate */ + if(H5CX_set_loc(dset_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set collective metadata read info") + /* Call private function to refresh the dataset object */ - if((H5D__refresh(dset_id, dset, H5AC_ind_read_dxpl_id)) < 0) + if((H5D__refresh(dset_id, dset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTLOAD, FAIL, "unable to refresh dataset") done: @@ -1019,11 +1015,15 @@ H5Dformat_convert(hid_t dset_id) if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + /* Set up collective metadata if appropriate */ + if(H5CX_set_loc(dset_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set collective metadata read info") + switch(dset->shared->layout.type) { case H5D_CHUNKED: /* Convert the chunk indexing type to version 1 B-tree if not */ if(dset->shared->layout.u.chunk.idx_type != H5D_CHUNK_IDX_BTREE) - if((H5D__format_convert(dset, H5AC_ind_read_dxpl_id)) < 0) + if((H5D__format_convert(dset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTLOAD, FAIL, "unable to downgrade chunk indexing type for dataset") break; @@ -1031,7 +1031,7 @@ H5Dformat_convert(hid_t dset_id) case H5D_COMPACT: /* Downgrade the layout version to 3 if greater than 3 */ if(dset->shared->layout.version > H5O_LAYOUT_VERSION_DEFAULT) - if((H5D__format_convert(dset, H5AC_ind_read_dxpl_id)) < 0) + if((H5D__format_convert(dset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTLOAD, FAIL, "unable to downgrade layout version for dataset") break; @@ -1089,3 +1089,44 @@ done: FUNC_LEAVE_API(ret_value) } /* H5Dget_chunk_index_type() */ + +/*------------------------------------------------------------------------- + * Function: H5Dget_chunk_storage_size + * + * Purpose: Returns the size of an allocated chunk. + * + * Return: Non-negative on success, negative on failure + * + * Programmer: Matthew Strong (GE Healthcare) + * 20 October 2016 + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_nbytes) +{ + H5D_t *dset = NULL; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_API(FAIL) + H5TRACE3("e", "i*h*h", dset_id, offset, chunk_nbytes); + + /* Check arguments */ + if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset") + if( NULL == offset ) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)") + if( NULL == chunk_nbytes ) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)") + + if(H5D_CHUNKED != dset->shared->layout.type) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset") + + /* Call private function */ + if(H5D__get_chunk_storage_size(dset, offset, chunk_nbytes) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get storage size of chunk") + +done: + FUNC_LEAVE_API(ret_value); +} /* H5Dget_chunk_storage_size() */ + |