diff options
Diffstat (limited to 'src/H5Dchunk.c')
| -rw-r--r-- | src/H5Dchunk.c | 216 |
1 files changed, 170 insertions, 46 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index e3bbd59..53ca7d1 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -254,6 +254,8 @@ static herr_t H5D__chunk_init(H5F_t *f, const H5D_t *dset, hid_t dapl_id); static herr_t H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *fm); +static herr_t H5D__chunk_io_init_selections(const H5D_io_info_t *io_info, + const H5D_type_info_t *type_info, H5D_chunk_map_t *fm); static herr_t H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *fm); @@ -297,6 +299,9 @@ static herr_t H5D__create_chunk_file_map_all(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info); static herr_t H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info); + +static herr_t H5D__create_chunk_mem_map_1d(const H5D_chunk_map_t *fm); + static herr_t H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm); static herr_t H5D__chunk_file_cb(void *elem, const H5T_t *type, unsigned ndims, const hsize_t *coords, void *fm); @@ -1095,7 +1100,6 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf H5D_chunk_map_t *fm) { const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ - const H5T_t *mem_type = type_info->mem_type; /* Local pointer to memory datatype */ H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */ hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */ htri_t file_space_normalized = FALSE; /* File dataspace was normalized */ @@ -1156,13 +1160,54 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf fm->file_space = file_space; fm->mem_space = mem_space; + if(H5D__chunk_io_init_selections(io_info, type_info, fm) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file and memory chunk selections") + +done: + /* Reset the global dataspace info */ + fm->file_space = NULL; + fm->mem_space = NULL; + + if(file_space_normalized == TRUE) + if(H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0) /* (Casting away const OK -QAK) */ + HDONE_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't denormalize selection") + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__chunk_io_init() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__chunk_io_init_selections + * + * Purpose: Initialize the chunk mappings + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Thursday, March 20, 2008 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__chunk_io_init_selections(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm) +{ + const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ + const H5T_t *mem_type = type_info->mem_type; /* Local pointer to memory datatype */ + H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */ + H5T_t *file_type = NULL; /* Temporary copy of file datatype for iteration */ + hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */ + char bogus; /* "bogus" buffer to pass to selection iterator */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + /* Special case for only one element in selection */ /* (usually appending a record) */ - if(nelmts == 1 + if(fm->nelmts == 1 #ifdef H5_HAVE_PARALLEL && !(io_info->using_mpi_vfd) #endif /* H5_HAVE_PARALLEL */ - && H5S_SEL_ALL != H5S_GET_SELECT_TYPE(file_space)) { + && H5S_SEL_ALL != H5S_GET_SELECT_TYPE(fm->file_space)) { /* Initialize skip list for chunk selections */ fm->sel_chunks = NULL; fm->use_single = TRUE; @@ -1170,7 +1215,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf /* Initialize single chunk dataspace */ if(NULL == dataset->shared->cache.chunk.single_space) { /* Make a copy of the dataspace for the dataset */ - if((dataset->shared->cache.chunk.single_space = H5S_copy(file_space, TRUE, FALSE)) == NULL) + if((dataset->shared->cache.chunk.single_space = H5S_copy(fm->file_space, TRUE, FALSE)) == NULL) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space") /* Resize chunk's dataspace dimensions to size of chunk */ @@ -1212,9 +1257,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf fm->use_single = FALSE; /* Get type of selection on disk & in memory */ - if((fm->fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE) + if((fm->fsel_type = H5S_GET_SELECT_TYPE(fm->file_space)) < H5S_SEL_NONE) HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection") - if((fm->msel_type = H5S_GET_SELECT_TYPE(mem_space)) < H5S_SEL_NONE) + if((fm->msel_type = H5S_GET_SELECT_TYPE(fm->mem_space)) < H5S_SEL_NONE) HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection") /* If the selection is NONE or POINTS, set the flag to FALSE */ @@ -1223,22 +1268,22 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf else sel_hyper_flag = TRUE; - /* Check if file selection is a not a hyperslab selection */ - if(sel_hyper_flag) { - /* Build the file selection for each chunk */ - if(H5S_SEL_ALL == fm->fsel_type) { - if(H5D__create_chunk_file_map_all(fm, io_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") + /* Check if file selection is a not a hyperslab selection */ + if(sel_hyper_flag) { + /* Build the file selection for each chunk */ + if(H5S_SEL_ALL == fm->fsel_type) { + if(H5D__create_chunk_file_map_all(fm, io_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") + } /* end if */ + else { + /* Sanity check */ + HDassert(fm->fsel_type == H5S_SEL_HYPERSLABS); + + if(H5D__create_chunk_file_map_hyper(fm, io_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") + } /* end else */ } /* end if */ else { - /* Sanity check */ - HDassert(fm->fsel_type == H5S_SEL_HYPERSLABS); - - if(H5D__create_chunk_file_map_hyper(fm, io_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") - } /* end else */ - } /* end if */ - else { H5S_sel_iter_op_t iter_op; /* Operator for iteration */ H5D_chunk_file_iter_ud_t udata; /* User data for iteration */ @@ -1256,7 +1301,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf iter_op.u.lib_op = H5D__chunk_file_cb; /* Spaces might not be the same shape, iterate over the file selection directly */ - if(H5S_select_iterate(&bogus, file_type, file_space, &iter_op, &udata) < 0) + if(H5S_select_iterate(&bogus, file_type, fm->file_space, &iter_op, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") /* Reset "last chunk" info */ @@ -1265,7 +1310,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf } /* end else */ /* Build the memory selection for each chunk */ - if(sel_hyper_flag && H5S_SELECT_SHAPE_SAME(file_space, mem_space) == TRUE) { + if(sel_hyper_flag && H5S_SELECT_SHAPE_SAME(fm->file_space, fm->mem_space) == TRUE) { /* Reset chunk template information */ fm->mchunk_tmpl = NULL; @@ -1275,12 +1320,19 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf if(H5D__create_chunk_mem_map_hyper(fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections") } /* end if */ - else { + else if(sel_hyper_flag && + fm->f_ndims == 1 && fm->m_ndims == 1 && + H5S_SELECT_IS_REGULAR(fm->mem_space) && H5S_SELECT_IS_SINGLE(fm->mem_space)) { + + if(H5D__create_chunk_mem_map_1d(fm) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") + + } else { H5S_sel_iter_op_t iter_op; /* Operator for iteration */ size_t elmt_size; /* Memory datatype size */ /* Make a copy of equivalent memory space */ - if((tmp_mspace = H5S_copy(mem_space, TRUE, FALSE)) == NULL) + if((tmp_mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == NULL) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") /* De-select the mem space copy */ @@ -1291,14 +1343,14 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf fm->mchunk_tmpl = tmp_mspace; /* Create temporary datatypes for selection iteration */ - if(!file_type) - if(NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL))) + if(!file_type) + if(NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype") /* Create selection iterator for memory selection */ if(0 == (elmt_size = H5T_get_size(mem_type))) HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid") - if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size, 0) < 0) + if(H5S_select_iter_init(&(fm->mem_iter), fm->mem_space, elmt_size, 0) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") iter_init = TRUE; /* Selection iteration info has been initialized */ @@ -1306,7 +1358,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf iter_op.u.lib_op = H5D__chunk_mem_cb; /* Spaces aren't the same shape, iterate over the memory selection directly */ - if(H5S_select_iterate(&bogus, file_type, file_space, &iter_op, fm) < 0) + if(H5S_select_iterate(&bogus, file_type, fm->file_space, &iter_op, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections") } /* end else */ } /* end else */ @@ -1323,20 +1375,13 @@ done: HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping") } /* end if */ - /* Reset the global dataspace info */ - fm->file_space = NULL; - fm->mem_space = NULL; - if(iter_init && H5S_SELECT_ITER_RELEASE(&(fm->mem_iter)) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator") if(file_type && (H5T_close_real(file_type) < 0)) HDONE_ERROR(H5E_DATATYPE, H5E_CANTFREE, FAIL, "Can't free temporary datatype") - if(file_space_normalized == TRUE) - if(H5S_hyper_denormalize_offset((H5S_t *)file_space, old_offset) < 0) /* (Casting away const OK -QAK) */ - HDONE_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't denormalize selection") FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__chunk_io_init() */ +} /* end H5D__chunk_io_init_selections() */ /*------------------------------------------------------------------------- @@ -2075,6 +2120,93 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__create_chunk_mem_map_hyper() */ + + +/*------------------------------------------------------------------------- + * Function: H5D__create_mem_map_1d + * + * Purpose: Create all chunk selections for 1-dimensional regular memory space + * that has only one single block in the selection + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Vailin Choi + * Sept 18, 2019 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__create_chunk_mem_map_1d(const H5D_chunk_map_t *fm) +{ + H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ + H5SL_node_t *curr_node; /* Current node in skip list */ + hsize_t file_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ + hsize_t file_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ + hsize_t mem_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ + hsize_t mem_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ + hssize_t adjust[H5S_MAX_RANK]; /* Adjustment to make to all file chunks */ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_STATIC + + /* Sanity check */ + HDassert(fm->f_ndims>0); + + /* Check for all I/O going to a single chunk */ + if(H5SL_count(fm->sel_chunks)==1) { + /* Get the node */ + curr_node = H5SL_first(fm->sel_chunks); + + /* Get pointer to chunk's information */ + chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); + HDassert(chunk_info); + + /* Just point at the memory dataspace & selection */ + /* (Casting away const OK -QAK) */ + chunk_info->mspace = (H5S_t *)fm->mem_space; + + /* Indicate that the chunk's memory space is shared */ + chunk_info->mspace_shared = TRUE; + } /* end if */ + else { + HDassert(fm->m_ndims == 1); + hsize_t mem_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ + hsize_t mem_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ + + if(H5S_SELECT_BOUNDS(fm->mem_space, mem_sel_start, mem_sel_end) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") + + /* Iterate over each chunk in the chunk list */ + curr_node = H5SL_first(fm->sel_chunks); + while(curr_node) { + hssize_t schunk_points; /* Number of elements in chunk selection */ + hsize_t tmp_count = 1; + + /* Get pointer to chunk's information */ + chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); + HDassert(chunk_info); + + /* Copy the memory dataspace */ + if((chunk_info->mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == NULL) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") + + schunk_points = H5S_GET_SELECT_NPOINTS(chunk_info->fspace); + + if(H5S_select_hyperslab(chunk_info->mspace, H5S_SELECT_SET, mem_sel_start, NULL, &tmp_count, &schunk_points) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't create chunk memory selection") + + mem_sel_start[0] += schunk_points; + + /* Get the next chunk node in the skip list */ + curr_node = H5SL_next(curr_node); + } /* end while */ + } /* end else */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__create_chunk_mem_map_1d() */ + /*------------------------------------------------------------------------- * Function: H5D__chunk_file_cb @@ -5956,23 +6088,15 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed") /* Reclaim space from variable length data */ - if(H5D_vlen_reclaim(tid_mem, buf_space, reclaim_buf) < 0) + if(H5T_reclaim(tid_mem, buf_space, reclaim_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, H5_ITER_ERROR, "unable to reclaim variable-length data") } /* end if */ else if(fix_ref) { /* Check for expanding references */ /* (background buffer has already been zeroed out, if not expanding) */ if(udata->cpy_info->expand_ref) { - size_t ref_count; - size_t dt_size; - - /* Determine # of reference elements to copy */ - if((dt_size = H5T_get_size(udata->dt_src)) == 0) - HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "size must not be 0") - ref_count = nbytes / dt_size; - /* Copy the reference elements */ - if(H5O_copy_expand_ref(udata->file_src, buf, udata->idx_info_dst->f, bkg, ref_count, H5T_get_ref_type(udata->dt_src), udata->cpy_info) < 0) + if(H5O_copy_expand_ref(udata->file_src, udata->tid_src, udata->dt_src, buf, nbytes, udata->idx_info_dst->f, bkg, udata->cpy_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, H5_ITER_ERROR, "unable to copy reference attribute") } /* end if */ |