diff options
Diffstat (limited to 'src/H5Dvirtual.c')
| -rw-r--r-- | src/H5Dvirtual.c | 202 |
1 files changed, 122 insertions, 80 deletions
diff --git a/src/H5Dvirtual.c b/src/H5Dvirtual.c index 04981c2..ee16a17 100644 --- a/src/H5Dvirtual.c +++ b/src/H5Dvirtual.c @@ -83,10 +83,9 @@ /* Layout operation callbacks */ static hbool_t H5D__virtual_is_data_cached(const H5D_shared_t *shared_dset); -static herr_t H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, - H5S_t *file_space, H5S_t *mem_space, H5D_chunk_map_t *fm); -static herr_t H5D__virtual_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, - H5S_t *file_space, H5S_t *mem_space, H5D_chunk_map_t *fm); +static herr_t H5D__virtual_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo); +static herr_t H5D__virtual_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo); +static herr_t H5D__virtual_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo); static herr_t H5D__virtual_flush(H5D_t *dset); /* Other functions */ @@ -103,13 +102,13 @@ static herr_t H5D__virtual_build_source_name(char size_t static_strlen, size_t nsubs, hsize_t blockno, char **built_name); static herr_t H5D__virtual_init_all(const H5D_t *dset); -static herr_t H5D__virtual_pre_io(H5D_io_info_t *io_info, H5O_storage_virtual_t *storage, H5S_t *file_space, - H5S_t *mem_space, hsize_t *tot_nelmts); +static herr_t H5D__virtual_pre_io(H5D_dset_io_info_t *dset_info, H5O_storage_virtual_t *storage, + H5S_t *file_space, H5S_t *mem_space, hsize_t *tot_nelmts); static herr_t H5D__virtual_post_io(H5O_storage_virtual_t *storage); -static herr_t H5D__virtual_read_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5S_t *file_space, H5O_storage_virtual_srcdset_t *source_dset); -static herr_t H5D__virtual_write_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5S_t *file_space, H5O_storage_virtual_srcdset_t *source_dset); +static herr_t H5D__virtual_read_one(H5D_dset_io_info_t *dset_info, + H5O_storage_virtual_srcdset_t *source_dset); +static herr_t H5D__virtual_write_one(H5D_dset_io_info_t *dset_info, + H5O_storage_virtual_srcdset_t *source_dset); /*********************/ /* Package Variables */ @@ -121,18 +120,15 @@ const H5D_layout_ops_t H5D_LOPS_VIRTUAL[1] = {{ H5D__virtual_init, /* init */ H5D__virtual_is_space_alloc, /* is_space_alloc */ H5D__virtual_is_data_cached, /* is_data_cached */ - NULL, /* io_init */ + H5D__virtual_io_init, /* io_init */ + NULL, /* mdio_init */ H5D__virtual_read, /* ser_read */ H5D__virtual_write, /* ser_write */ -#ifdef H5_HAVE_PARALLEL - NULL, /* par_read */ - NULL, /* par_write */ -#endif - NULL, /* readvv */ - NULL, /* writevv */ - H5D__virtual_flush, /* flush */ - NULL, /* io_term */ - NULL /* dest */ + NULL, /* readvv */ + NULL, /* writevv */ + H5D__virtual_flush, /* flush */ + NULL, /* io_term */ + NULL /* dest */ }}; /*******************/ @@ -2371,6 +2367,29 @@ done: } /* end H5D__virtual_is_data_cached() */ /*------------------------------------------------------------------------- + * Function: H5D__virtual_io_init + * + * Purpose: Performs initialization before any sort of I/O on the raw data + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner + * Sunday, May 22, 2022 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D__virtual_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t H5_ATTR_UNUSED *dinfo) +{ + FUNC_ENTER_PACKAGE_NOERR + + /* Disable selection I/O */ + io_info->use_select_io = FALSE; + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5D__virtual_io_init() */ + +/*------------------------------------------------------------------------- * Function: H5D__virtual_pre_io * * Purpose: Project all virtual mappings onto mem_space, with the @@ -2386,16 +2405,17 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__virtual_pre_io(H5D_io_info_t *io_info, H5O_storage_virtual_t *storage, H5S_t *file_space, +H5D__virtual_pre_io(H5D_dset_io_info_t *dset_info, H5O_storage_virtual_t *storage, H5S_t *file_space, H5S_t *mem_space, hsize_t *tot_nelmts) { - hssize_t select_nelmts; /* Number of elements in selection */ - hsize_t bounds_start[H5S_MAX_RANK]; /* Selection bounds start */ - hsize_t bounds_end[H5S_MAX_RANK]; /* Selection bounds end */ - int rank = 0; - hbool_t bounds_init = FALSE; /* Whether bounds_start, bounds_end, and rank are valid */ - size_t i, j, k; /* Local index variables */ - herr_t ret_value = SUCCEED; /* Return value */ + const H5D_t *dset = dset_info->dset; /* Local pointer to dataset info */ + hssize_t select_nelmts; /* Number of elements in selection */ + hsize_t bounds_start[H5S_MAX_RANK]; /* Selection bounds start */ + hsize_t bounds_end[H5S_MAX_RANK]; /* Selection bounds end */ + int rank = 0; + hbool_t bounds_init = FALSE; /* Whether bounds_start, bounds_end, and rank are valid */ + size_t i, j, k; /* Local index variables */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -2407,7 +2427,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, H5O_storage_virtual_t *storage, H5S_ /* Initialize layout if necessary */ if (!storage->init) - if (H5D__virtual_init_all(io_info->dset) < 0) + if (H5D__virtual_init_all(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize virtual layout") /* Initialize tot_nelmts */ @@ -2427,7 +2447,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, H5O_storage_virtual_t *storage, H5S_ /* Get selection bounds if necessary */ if (!bounds_init) { /* Get rank of VDS */ - if ((rank = H5S_GET_EXTENT_NDIMS(io_info->dset->shared->space)) < 0) + if ((rank = H5S_GET_EXTENT_NDIMS(dset->shared->space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get number of dimensions") /* Get selection bounds */ @@ -2469,7 +2489,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, H5O_storage_virtual_t *storage, H5S_ * open the source dataset to patch it */ if (storage->list[i].source_space_status != H5O_VIRTUAL_STATUS_CORRECT) { HDassert(!storage->list[i].sub_dset[j].dset); - if (H5D__virtual_open_source_dset(io_info->dset, &storage->list[i], + if (H5D__virtual_open_source_dset(dset, &storage->list[i], &storage->list[i].sub_dset[j]) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open source dataset") } /* end if */ @@ -2499,7 +2519,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, H5O_storage_virtual_t *storage, H5S_ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") /* Get current VDS dimensions */ - if (H5S_get_simple_extent_dims(io_info->dset->shared->space, tmp_dims, NULL) < 0) + if (H5S_get_simple_extent_dims(dset->shared->space, tmp_dims, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get VDS dimensions") /* Copy virtual selection */ @@ -2554,7 +2574,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, H5O_storage_virtual_t *storage, H5S_ /* Open source dataset */ if (!storage->list[i].sub_dset[j].dset) /* Try to open dataset */ - if (H5D__virtual_open_source_dset(io_info->dset, &storage->list[i], + if (H5D__virtual_open_source_dset(dset, &storage->list[i], &storage->list[i].sub_dset[j]) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open source dataset") @@ -2599,7 +2619,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, H5O_storage_virtual_t *storage, H5S_ /* Open source dataset */ if (!storage->list[i].source_dset.dset) /* Try to open dataset */ - if (H5D__virtual_open_source_dset(io_info->dset, &storage->list[i], + if (H5D__virtual_open_source_dset(dset, &storage->list[i], &storage->list[i].source_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open source dataset") @@ -2697,11 +2717,11 @@ H5D__virtual_post_io(H5O_storage_virtual_t *storage) *------------------------------------------------------------------------- */ static herr_t -H5D__virtual_read_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5S_t *file_space, - H5O_storage_virtual_srcdset_t *source_dset) +H5D__virtual_read_one(H5D_dset_io_info_t *dset_info, H5O_storage_virtual_srcdset_t *source_dset) { - H5S_t *projected_src_space = NULL; /* File space for selection in a single source dataset */ - herr_t ret_value = SUCCEED; /* Return value */ + H5S_t *projected_src_space = NULL; /* File space for selection in a single source dataset */ + H5D_dset_io_info_t source_dinfo; /* Dataset info for source dataset read */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -2717,15 +2737,23 @@ H5D__virtual_read_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, /* Project intersection of file space and mapping virtual space onto * mapping source space */ if (H5S_select_project_intersection(source_dset->clipped_virtual_select, - source_dset->clipped_source_select, file_space, + source_dset->clipped_source_select, dset_info->file_space, &projected_src_space, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto source space") - /* Perform read on source dataset */ - if (H5D__read(source_dset->dset, type_info->dst_type_id, source_dset->projected_mem_space, - projected_src_space, io_info->u.rbuf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read source dataset") + { + /* Initialize source_dinfo */ + source_dinfo.dset = source_dset->dset; + source_dinfo.mem_space = source_dset->projected_mem_space; + source_dinfo.file_space = projected_src_space; + source_dinfo.buf.vp = dset_info->buf.vp; + source_dinfo.mem_type_id = dset_info->type_info.dst_type_id; + + /* Read in the point (with the custom VL memory allocator) */ + if (H5D__read(1, &source_dinfo) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read source dataset") + } /* Close projected_src_space */ if (H5S_close(projected_src_space) < 0) @@ -2734,7 +2762,7 @@ H5D__virtual_read_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, } /* end if */ done: - /* Release allocated resources on failure */ + /* Release allocated resources */ if (projected_src_space) { HDassert(ret_value < 0); if (H5S_close(projected_src_space) < 0) @@ -2757,12 +2785,12 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, H5S_t *file_space, - H5S_t *mem_space, H5D_chunk_map_t H5_ATTR_UNUSED *fm) +H5D__virtual_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) { H5O_storage_virtual_t *storage; /* Convenient pointer into layout struct */ hsize_t tot_nelmts; /* Total number of elements mapped to mem_space */ H5S_t *fill_space = NULL; /* Space to fill with fill value */ + size_t nelmts; /* Number of elements to process */ size_t i, j; /* Local index variables */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2770,22 +2798,25 @@ H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsiz /* Sanity check */ HDassert(io_info); - HDassert(io_info->u.rbuf); - HDassert(type_info); - HDassert(mem_space); - HDassert(file_space); + HDassert(dset_info); + HDassert(dset_info->buf.vp); + HDassert(dset_info->mem_space); + HDassert(dset_info->file_space); - storage = &io_info->dset->shared->layout.storage.u.virt; + storage = &(dset_info->dset->shared->layout.storage.u.virt); HDassert((storage->view == H5D_VDS_FIRST_MISSING) || (storage->view == H5D_VDS_LAST_AVAILABLE)); + /* Initialize nelmts */ + nelmts = H5S_GET_SELECT_NPOINTS(dset_info->file_space); + #ifdef H5_HAVE_PARALLEL /* Parallel reads are not supported (yet) */ - if (H5F_HAS_FEATURE(io_info->dset->oloc.file, H5FD_FEAT_HAS_MPI)) + if (H5F_HAS_FEATURE(dset_info->dset->oloc.file, H5FD_FEAT_HAS_MPI)) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "parallel reads not supported on virtual datasets") #endif /* H5_HAVE_PARALLEL */ /* Prepare for I/O operation */ - if (H5D__virtual_pre_io(io_info, storage, file_space, mem_space, &tot_nelmts) < 0) + if (H5D__virtual_pre_io(dset_info, storage, dset_info->file_space, dset_info->mem_space, &tot_nelmts) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to prepare for I/O operation") /* Iterate over mappings */ @@ -2797,12 +2828,12 @@ H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsiz if (storage->list[i].psfn_nsubs || storage->list[i].psdn_nsubs) { /* Iterate over sub-source dsets */ for (j = storage->list[i].sub_dset_io_start; j < storage->list[i].sub_dset_io_end; j++) - if (H5D__virtual_read_one(io_info, type_info, file_space, &storage->list[i].sub_dset[j]) < 0) + if (H5D__virtual_read_one(dset_info, &storage->list[i].sub_dset[j]) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read source dataset") } /* end if */ else /* Read from source dataset */ - if (H5D__virtual_read_one(io_info, type_info, file_space, &storage->list[i].source_dset) < 0) + if (H5D__virtual_read_one(dset_info, &storage->list[i].source_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read source dataset") } /* end for */ @@ -2811,13 +2842,13 @@ H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsiz H5D_fill_value_t fill_status; /* Fill value status */ /* Check the fill value status */ - if (H5P_is_fill_value_defined(&io_info->dset->shared->dcpl_cache.fill, &fill_status) < 0) + if (H5P_is_fill_value_defined(&dset_info->dset->shared->dcpl_cache.fill, &fill_status) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* Always write fill value to memory buffer unless it is undefined */ if (fill_status != H5D_FILL_VALUE_UNDEFINED) { /* Start with fill space equal to memory space */ - if (NULL == (fill_space = H5S_copy(mem_space, FALSE, TRUE))) + if (NULL == (fill_space = H5S_copy(dset_info->mem_space, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy memory selection") /* Iterate over mappings */ @@ -2837,8 +2868,8 @@ H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsiz HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to clip fill selection") /* Write fill values to memory buffer */ - if (H5D__fill(io_info->dset->shared->dcpl_cache.fill.buf, io_info->dset->shared->type, - io_info->u.rbuf, type_info->mem_type, fill_space) < 0) + if (H5D__fill(dset_info->dset->shared->dcpl_cache.fill.buf, dset_info->dset->shared->type, + dset_info->buf.vp, dset_info->type_info.mem_type, fill_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "filling buf failed") #ifndef NDEBUG @@ -2887,11 +2918,11 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__virtual_write_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5S_t *file_space, - H5O_storage_virtual_srcdset_t *source_dset) +H5D__virtual_write_one(H5D_dset_io_info_t *dset_info, H5O_storage_virtual_srcdset_t *source_dset) { - H5S_t *projected_src_space = NULL; /* File space for selection in a single source dataset */ - herr_t ret_value = SUCCEED; /* Return value */ + H5S_t *projected_src_space = NULL; /* File space for selection in a single source dataset */ + H5D_dset_io_info_t source_dinfo; /* Dataset info for source dataset write */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -2909,15 +2940,23 @@ H5D__virtual_write_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, /* Project intersection of file space and mapping virtual space onto * mapping source space */ if (H5S_select_project_intersection(source_dset->clipped_virtual_select, - source_dset->clipped_source_select, file_space, + source_dset->clipped_source_select, dset_info->file_space, &projected_src_space, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto source space") - /* Perform write on source dataset */ - if (H5D__write(source_dset->dset, type_info->dst_type_id, source_dset->projected_mem_space, - projected_src_space, io_info->u.wbuf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write to source dataset") + { + /* Initialize source_dinfo */ + source_dinfo.dset = source_dset->dset; + source_dinfo.mem_space = source_dset->projected_mem_space; + source_dinfo.file_space = projected_src_space; + source_dinfo.buf.cvp = dset_info->buf.cvp; + source_dinfo.mem_type_id = dset_info->type_info.dst_type_id; + + /* Read in the point (with the custom VL memory allocator) */ + if (H5D__write(1, &source_dinfo) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read source dataset") + } /* Close projected_src_space */ if (H5S_close(projected_src_space) < 0) @@ -2926,7 +2965,7 @@ H5D__virtual_write_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, } /* end if */ done: - /* Release allocated resources on failure */ + /* Release allocated resources */ if (projected_src_space) { HDassert(ret_value < 0); if (H5S_close(projected_src_space) < 0) @@ -2949,11 +2988,11 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__virtual_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, - H5S_t *file_space, H5S_t *mem_space, H5D_chunk_map_t H5_ATTR_UNUSED *fm) +H5D__virtual_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) { H5O_storage_virtual_t *storage; /* Convenient pointer into layout struct */ hsize_t tot_nelmts; /* Total number of elements mapped to mem_space */ + size_t nelmts; /* Number of elements to process */ size_t i, j; /* Local index variables */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2961,22 +3000,25 @@ H5D__virtual_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsi /* Sanity check */ HDassert(io_info); - HDassert(io_info->u.wbuf); - HDassert(type_info); - HDassert(mem_space); - HDassert(file_space); + HDassert(dset_info); + HDassert(dset_info->buf.cvp); + HDassert(dset_info->mem_space); + HDassert(dset_info->file_space); - storage = &io_info->dset->shared->layout.storage.u.virt; + storage = &(dset_info->dset->shared->layout.storage.u.virt); HDassert((storage->view == H5D_VDS_FIRST_MISSING) || (storage->view == H5D_VDS_LAST_AVAILABLE)); + /* Initialize nelmts */ + nelmts = H5S_GET_SELECT_NPOINTS(dset_info->file_space); + #ifdef H5_HAVE_PARALLEL /* Parallel writes are not supported (yet) */ - if (H5F_HAS_FEATURE(io_info->dset->oloc.file, H5FD_FEAT_HAS_MPI)) + if (H5F_HAS_FEATURE(dset_info->dset->oloc.file, H5FD_FEAT_HAS_MPI)) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "parallel writes not supported on virtual datasets") #endif /* H5_HAVE_PARALLEL */ /* Prepare for I/O operation */ - if (H5D__virtual_pre_io(io_info, storage, file_space, mem_space, &tot_nelmts) < 0) + if (H5D__virtual_pre_io(dset_info, storage, dset_info->file_space, dset_info->mem_space, &tot_nelmts) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to prepare for I/O operation") /* Fail if there are unmapped parts of the selection as they would not be @@ -2994,12 +3036,12 @@ H5D__virtual_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsi if (storage->list[i].psfn_nsubs || storage->list[i].psdn_nsubs) { /* Iterate over sub-source dsets */ for (j = storage->list[i].sub_dset_io_start; j < storage->list[i].sub_dset_io_end; j++) - if (H5D__virtual_write_one(io_info, type_info, file_space, &storage->list[i].sub_dset[j]) < 0) + if (H5D__virtual_write_one(dset_info, &storage->list[i].sub_dset[j]) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write to source dataset") } /* end if */ else /* Write to source dataset */ - if (H5D__virtual_write_one(io_info, type_info, file_space, &storage->list[i].source_dset) < 0) + if (H5D__virtual_write_one(dset_info, &storage->list[i].source_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write to source dataset") } /* end for */ |