diff options
Diffstat (limited to 'src/H5Dint.c')
| -rw-r--r-- | src/H5Dint.c | 245 |
1 files changed, 219 insertions, 26 deletions
diff --git a/src/H5Dint.c b/src/H5Dint.c index 8815819..96b1dbd 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -43,16 +43,34 @@ /* Local Typedefs */ /******************/ -/* Internal data structure for computing variable-length dataset's total size */ +/* Shared data structure for computing variable-length dataset's total size */ +/* (Used for both native and generic 'get vlen buf size' operation) */ 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; +} H5D_vlen_bufsize_common_t; + +/* Internal data structure for computing variable-length dataset's total size */ +/* (Used for native 'get vlen buf size' operation) */ +typedef struct { + H5D_t *dset; /* Dataset for operation */ + H5S_t *fspace; /* Dataset's dataspace for operation */ + H5S_t *mspace; /* Memory dataspace for operation */ + H5D_vlen_bufsize_common_t common; /* VL data buffers & accumulatd size */ +} H5D_vlen_bufsize_native_t; + +/* Internal data structure for computing variable-length dataset's total size */ +/* (Used for generic 'get vlen buf size' operation) */ +typedef struct { + H5VL_object_t *dset_vol_obj; /* VOL object for the dataset */ + hid_t fspace_id; /* Dataset dataspace ID of the dataset we are working on */ + H5S_t *fspace; /* Dataset's dataspace for operation */ + hid_t mspace_id; /* Memory dataspace ID of the dataset we are working on */ + hid_t dxpl_id; /* Dataset transfer property list to pass to dataset read */ + H5D_vlen_bufsize_common_t common; /* VL data buffers & accumulatd size */ +} H5D_vlen_bufsize_generic_t; /********************/ @@ -77,6 +95,8 @@ static size_t H5D__calculate_minimum_header_size(H5F_t *file, H5D_t *dset, H5O_t 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); +static herr_t H5D__vlen_get_buf_size_gen_cb(void *elem, hid_t type_id, unsigned ndim, + const hsize_t *point, void *op_data); /*********************/ @@ -2591,23 +2611,23 @@ done: static void * H5D__vlen_get_buf_size_alloc(size_t size, void *info) { - H5D_vlen_bufsize_t *vlen_bufsize = (H5D_vlen_bufsize_t *)info; + H5D_vlen_bufsize_common_t *vlen_bufsize_com = (H5D_vlen_bufsize_common_t *)info; void *ret_value = NULL; /* Return value */ 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))) + if(size > vlen_bufsize_com->vl_tbuf_size) { + if(NULL == (vlen_bufsize_com->vl_tbuf = H5FL_BLK_REALLOC(vlen_vl_buf, vlen_bufsize_com->vl_tbuf, size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, NULL, "can't reallocate temporary VL data buffer") - vlen_bufsize->vl_tbuf_size = size; + vlen_bufsize_com->vl_tbuf_size = size; } /* end if */ /* Increment size of VL data buffer needed */ - vlen_bufsize->size += size; + vlen_bufsize_com->size += size; /* Set return value */ - ret_value = vlen_bufsize->vl_tbuf; + ret_value = vlen_bufsize_com->vl_tbuf; done: FUNC_LEAVE_NOAPI(ret_value) @@ -2627,7 +2647,7 @@ 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; + H5D_vlen_bufsize_native_t *vlen_bufsize = (H5D_vlen_bufsize_native_t *)op_data; herr_t ret_value = H5_ITER_CONT; /* Return value */ FUNC_ENTER_STATIC @@ -2642,7 +2662,7 @@ H5D__vlen_get_buf_size_cb(void H5_ATTR_UNUSED *elem, hid_t type_id, 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) + if(H5D__read(vlen_bufsize->dset, type_id, vlen_bufsize->mspace, vlen_bufsize->fspace, vlen_bufsize->common.fl_tbuf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, H5_ITER_ERROR, "can't read point") done: @@ -2678,7 +2698,7 @@ herr_t 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 = {NULL, NULL, NULL, NULL, NULL, 0, 0}; + H5D_vlen_bufsize_native_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() */ @@ -2690,9 +2710,9 @@ H5D__vlen_get_buf_size(H5D_t *dset, hid_t type_id, hid_t space_id, FUNC_ENTER_PACKAGE /* Check args */ - if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE))) + if(NULL == (type = (H5T_t *)H5I_object(type_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an valid base datatype") - if(NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))) + if(NULL == (space = (H5S_t *)H5I_object(space_id))) 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") @@ -2711,18 +2731,18 @@ H5D__vlen_get_buf_size(H5D_t *dset, hid_t type_id, hid_t space_id, 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)))) + if(NULL == (vlen_bufsize.common.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))) + if(NULL == (vlen_bufsize.common.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; + vlen_bufsize.common.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) + if(H5CX_set_vlen_alloc_info(H5D__vlen_get_buf_size_alloc, &vlen_bufsize.common, 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; + vlen_bufsize.common.size = 0; /* Call H5S_select_iterate with args, etc. */ dset_op.op_type = H5S_SEL_ITER_OP_APP; @@ -2733,23 +2753,196 @@ H5D__vlen_get_buf_size(H5D_t *dset, hid_t type_id, hid_t space_id, /* Get the size if we succeeded */ if(ret_value >= 0) - *size = vlen_bufsize.size; + *size = vlen_bufsize.common.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); + if(vlen_bufsize.common.fl_tbuf != NULL) + vlen_bufsize.common.fl_tbuf = H5FL_BLK_FREE(vlen_fl_buf, vlen_bufsize.common.fl_tbuf); + if(vlen_bufsize.common.vl_tbuf != NULL) + vlen_bufsize.common.vl_tbuf = H5FL_BLK_FREE(vlen_vl_buf, vlen_bufsize.common.vl_tbuf); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__vlen_get_buf_size() */ /*------------------------------------------------------------------------- + * Function: H5D__vlen_get_buf_size_gen_cb + * + * 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 + *------------------------------------------------------------------------- + */ +static herr_t +H5D__vlen_get_buf_size_gen_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_generic_t *vlen_bufsize = (H5D_vlen_bufsize_generic_t *)op_data; + H5T_t *dt; /* Datatype for operation */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity check */ + HDassert(point); + HDassert(op_data); + + /* 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->common.fl_tbuf = H5FL_BLK_REALLOC(vlen_fl_buf, vlen_bufsize->common.fl_tbuf, H5T_get_size(dt)))) + HGOTO_ERROR(H5E_DATASET, H5E_NOSPACE, FAIL, "can't resize tbuf") + + /* 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, FAIL, "can't select point") + + /* Read in the point (with the custom VL memory allocator) */ + if(H5VL_dataset_read(vlen_bufsize->dset_vol_obj, type_id, vlen_bufsize->mspace_id, vlen_bufsize->fspace_id, vlen_bufsize->dxpl_id, vlen_bufsize->common.fl_tbuf, H5_REQUEST_NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__vlen_get_buf_size_gen_cb() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__vlen_get_buf_size_gen + * + * Purpose: Generic routine to checks the number of bytes required to store the + * VL data from the dataset. + * + * Return: Non-negative on success, negative on failure + * + * Programmer: Quincey Koziol + * Friday, December 20, 2019 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D__vlen_get_buf_size_gen(H5VL_object_t *vol_obj, hid_t type_id, hid_t space_id, + hsize_t *size) +{ + H5D_vlen_bufsize_generic_t vlen_bufsize = {NULL, H5I_INVALID_HID, NULL, H5I_INVALID_HID, H5I_INVALID_HID, {NULL, NULL, 0, 0}}; + H5P_genplist_t *dxpl = NULL; /* DXPL for operation */ + 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 = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Check args */ + if(NULL == (type = (H5T_t *)H5I_object(type_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not an valid datatype") + if(NULL == (space = (H5S_t *)H5I_object(space_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "invalid dataspace") + if(!(H5S_has_extent(space))) + HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "dataspace does not have extent set") + + /* Save the dataset */ + vlen_bufsize.dset_vol_obj = vol_obj; + + /* Get a copy of the dataset's dataspace */ + if(H5VL_dataset_get(vol_obj, H5VL_DATASET_GET_SPACE, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, &vlen_bufsize.fspace_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace") + if(NULL == (vlen_bufsize.fspace = (H5S_t *)H5I_object(vlen_bufsize.fspace_id))) + HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "not a dataspace") + + /* Create a scalar for the memory dataspace */ + if(NULL == (mspace = H5S_create(H5S_SCALAR))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create dataspace") + if((vlen_bufsize.mspace_id = H5I_register(H5I_DATASPACE, mspace, TRUE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID") + + /* Grab the temporary buffers required */ + if(NULL == (vlen_bufsize.common.fl_tbuf = H5FL_BLK_MALLOC(vlen_fl_buf, H5T_get_size(type)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "no temporary buffers available") + if(NULL == (vlen_bufsize.common.vl_tbuf = H5FL_BLK_MALLOC(vlen_vl_buf, (size_t)1))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "no temporary buffers available") + vlen_bufsize.common.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.common, NULL, NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set VL data allocation routine") + + /* Set the VL allocation callbacks on a DXPL */ + if(NULL == (dxpl = (H5P_genplist_t *)H5I_object(H5P_DATASET_XFER_DEFAULT))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get default DXPL") + if((vlen_bufsize.dxpl_id = H5P_copy_plist(dxpl, TRUE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy property list"); + if(NULL == (dxpl = (H5P_genplist_t *)H5I_object(vlen_bufsize.dxpl_id))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get copied DXPL") + if(H5P_set_vlen_mem_manager(dxpl, H5D__vlen_get_buf_size_alloc, &vlen_bufsize.common, NULL, NULL) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set VL data allocation routine on DXPL") + + /* Set the initial number of bytes required */ + vlen_bufsize.common.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_gen_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.common.size; + +done: + if(vlen_bufsize.fspace_id >= 0) { + if(H5I_dec_app_ref(vlen_bufsize.fspace_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "problem freeing id") + vlen_bufsize.fspace = NULL; + } /* end if */ + if(vlen_bufsize.fspace && H5S_close(vlen_bufsize.fspace) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + if(vlen_bufsize.mspace_id >= 0) { + if(H5I_dec_app_ref(vlen_bufsize.mspace_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "problem freeing id") + mspace = NULL; + } /* end if */ + if(mspace && H5S_close(mspace) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release dataspace") + if(vlen_bufsize.common.fl_tbuf != NULL) + vlen_bufsize.common.fl_tbuf = H5FL_BLK_FREE(vlen_fl_buf, vlen_bufsize.common.fl_tbuf); + if(vlen_bufsize.common.vl_tbuf != NULL) + vlen_bufsize.common.vl_tbuf = H5FL_BLK_FREE(vlen_vl_buf, vlen_bufsize.common.vl_tbuf); + if(vlen_bufsize.dxpl_id != H5I_INVALID_HID) { + if(H5I_dec_app_ref(vlen_bufsize.dxpl_id) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't close property list") + dxpl = NULL; + } /* end if */ + if(dxpl && H5P_close(dxpl) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release DXPL") + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__vlen_get_buf_size_gen() */ + + +/*------------------------------------------------------------------------- * Function: H5D__check_filters * * Purpose: Check if the filters have be initialized for the dataset |