diff options
Diffstat (limited to 'src/H5Dint.c')
| -rw-r--r-- | src/H5Dint.c | 182 |
1 files changed, 142 insertions, 40 deletions
diff --git a/src/H5Dint.c b/src/H5Dint.c index c3d4398..8815819 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -43,6 +43,17 @@ /* Local Typedefs */ /******************/ +/* Internal data structure for computing variable-length dataset's total size */ +typedef struct { + H5D_t *dset; /* Dataset for operation */ + H5S_t *fspace; /* Dataset's dataspace for operation */ + H5S_t *mspace; /* Memory dataspace for operation */ + void *fl_tbuf; /* Ptr to the temporary buffer we are using for fixed-length data */ + void *vl_tbuf; /* Ptr to the temporary buffer we are using for VL data */ + size_t vl_tbuf_size; /* Current size of the temp. buffer for VL data */ + hsize_t size; /* Accumulated number of bytes for the selection */ +} H5D_vlen_bufsize_t; + /********************/ /* Local Prototypes */ @@ -63,6 +74,9 @@ static herr_t H5D__close_cb(H5VL_object_t *dset_vol_obj); static herr_t H5D__use_minimized_dset_headers(H5F_t *file, H5D_t *dset, hbool_t *minimize); static herr_t H5D__prepare_minimized_oh(H5F_t *file, H5D_t *dset, H5O_loc_t *oloc); static size_t H5D__calculate_minimum_header_size(H5F_t *file, H5D_t *dset, H5O_t *ohdr); +static void *H5D__vlen_get_buf_size_alloc(size_t size, void *info); +static herr_t H5D__vlen_get_buf_size_cb(void *elem, hid_t type_id, unsigned ndim, + const hsize_t *point, void *op_data); /*********************/ @@ -98,8 +112,12 @@ H5FL_EXTERN(H5D_chunk_info_t); /* Declare extern the free list to manage blocks of type conversion data */ H5FL_BLK_EXTERN(type_conv); +/* Disable warning for intentional identical branches here -QAK */ +#pragma GCC diagnostic push +#pragma GCC diagnostic ignored "-Wlarger-than=" /* Define a static "default" dataset structure to use to initialize new datasets */ static H5D_shared_t H5D_def_dset; +#pragma GCC diagnostic pop /* Dataset ID class */ static const H5I_class_t H5I_DATASET_CLS[1] = {{ @@ -113,7 +131,7 @@ static const H5I_class_t H5I_DATASET_CLS[1] = {{ static hbool_t H5D_top_package_initialize_s = FALSE; /* Prefixes of VDS and external file from the environment variables - * HDF5_EXTFILE_PREFIX and HDF5_VDS_PREFIX */ + * HDF5_EXTFILE_PREFIX and HDF5_VDS_PREFIX */ static const char *H5D_prefix_ext_env = NULL; static const char *H5D_prefix_vds_env = NULL; @@ -2567,36 +2585,79 @@ done: * this data is not actually usable. * * Return: Non-negative on success, negative on failure + * *------------------------------------------------------------------------- */ -void * +static void * H5D__vlen_get_buf_size_alloc(size_t size, void *info) { H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)info; void *ret_value = NULL; /* Return value */ - FUNC_ENTER_PACKAGE_NOERR + FUNC_ENTER_STATIC + + /* Check for increasing the size of the temporary space for VL data */ + if(size > vlen_bufsize->vl_tbuf_size) { + if(NULL == (vlen_bufsize->vl_tbuf = H5FL_BLK_REALLOC(vlen_vl_buf, vlen_bufsize->vl_tbuf, size))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't reallocate temporary VL data buffer") + vlen_bufsize->vl_tbuf_size = size; + } /* end if */ - /* 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; + /* Increment size of VL data buffer needed */ + vlen_bufsize->size += size; /* Set return value */ ret_value = vlen_bufsize->vl_tbuf; +done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__vlen_get_buf_size_alloc() */ /*------------------------------------------------------------------------- - * Function: H5D__vlen_get_buf_size + * Function: H5D__vlen_get_buf_size_cb + * + * Purpose: Dataspace selection iteration callback for H5Dvlen_get_buf_size. + * + * Return: Non-negative on success, negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__vlen_get_buf_size_cb(void H5_ATTR_UNUSED *elem, hid_t type_id, + unsigned H5_ATTR_UNUSED ndim, const hsize_t *point, void *op_data) +{ + H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)op_data; + herr_t ret_value = H5_ITER_CONT; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity check */ + HDassert(H5I_DATATYPE == H5I_get_type(type_id)); + HDassert(point); + HDassert(op_data); + + /* Select point to read in */ + if(H5S_select_elements(vlen_bufsize->fspace, H5S_SELECT_SET, (size_t)1, point) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, H5_ITER_ERROR, "can't select point") + + /* Read in the point (with the custom VL memory allocator) */ + if(H5D__read(vlen_bufsize->dset, type_id, vlen_bufsize->mspace, vlen_bufsize->fspace, vlen_bufsize->fl_tbuf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "can't read point") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__vlen_get_buf_size_cb() */ + + +/*------------------------------------------------------------------------- + * 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. + * 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 @@ -2606,43 +2667,84 @@ H5D__vlen_get_buf_size_alloc(size_t size, void *info) * 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 + * Return: Non-negative on success, negative on failure + * + * Programmer: Quincey Koziol + * Wednesday, August 11, 1999 + * *------------------------------------------------------------------------- */ herr_t -H5D__vlen_get_buf_size(void H5_ATTR_UNUSED *elem, hid_t type_id, - unsigned H5_ATTR_UNUSED ndim, const hsize_t *point, void *op_data) +H5D__vlen_get_buf_size(H5D_t *dset, hid_t type_id, hid_t space_id, + hsize_t *size) { - H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)op_data; - H5VL_object_t *vol_obj = vlen_bufsize->dset_vol_obj; - H5T_t *dt; /* Datatype for operation */ - H5S_t *fspace; /* File dataspace for operation */ - herr_t ret_value = SUCCEED; /* Return value */ + H5D_vlen_bufsize_t vlen_bufsize = {NULL, NULL, NULL, NULL, NULL, 0, 0}; + 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 */ + H5T_t *type; /* Datatype */ + H5S_sel_iter_op_t dset_op; /* Operator for iteration */ + herr_t ret_value = FAIL; /* Return value */ FUNC_ENTER_PACKAGE - HDassert(op_data); - HDassert(H5I_DATATYPE == H5I_get_type(type_id)); - /* Check args */ - if(NULL == (dt = (H5T_t *)H5I_object(type_id))) - HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not a datatype") - - /* Make certain there is enough fixed-length buffer available */ - if(NULL == (vlen_bufsize->fl_tbuf = H5FL_BLK_REALLOC(vlen_fl_buf, vlen_bufsize->fl_tbuf, H5T_get_size(dt)))) - HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, FAIL, "can't resize tbuf") - - /* Select point to read in */ - if(NULL == (fspace = (H5S_t *)H5I_object_verify(vlen_bufsize->fspace_id, H5I_DATASPACE))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace") - if(H5S_select_elements(fspace, H5S_SELECT_SET, (size_t)1, point) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't select point") - - /* Read in the point (with the custom VL memory allocator) */ - if(H5VL_dataset_read(vol_obj, type_id, vlen_bufsize->mspace_id, vlen_bufsize->fspace_id, vlen_bufsize->dxpl_id, vlen_bufsize->fl_tbuf, H5_REQUEST_NULL) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point") + if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype") + if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace") + if(!(H5S_has_extent(space))) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspace does not have extent set") + + /* Save the dataset */ + vlen_bufsize.dset = dset; + + /* Get a copy of the dataset's dataspace */ + if(NULL == (fspace = H5S_copy(dset->shared->space, FALSE, TRUE))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to get dataspace") + vlen_bufsize.fspace = fspace; + + /* Create a scalar for the memory dataspace */ + if(NULL == (mspace = H5S_create(H5S_SCALAR))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create dataspace") + vlen_bufsize.mspace = mspace; + + /* Grab the temporary buffers required */ + if(NULL == (vlen_bufsize.fl_tbuf = H5FL_BLK_MALLOC(vlen_fl_buf, H5T_get_size(type)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available") + 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") + vlen_bufsize.vl_tbuf_size = 1; + + /* Set the memory manager to the special 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; + + /* Call H5S_select_iterate with args, etc. */ + dset_op.op_type = H5S_SEL_ITER_OP_APP; + dset_op.u.app_op.op = H5D__vlen_get_buf_size_cb; + dset_op.u.app_op.type_id = type_id; + + ret_value = H5S_select_iterate(&bogus, type, space, &dset_op, &vlen_bufsize); + + /* Get the size if we succeeded */ + if(ret_value >= 0) + *size = vlen_bufsize.size; done: + if(fspace && H5S_close(fspace) < 0) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + if(mspace && H5S_close(mspace) < 0) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + if(vlen_bufsize.fl_tbuf != NULL) + 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); + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__vlen_get_buf_size() */ |