diff options
Diffstat (limited to 'src/H5Dvirtual.c')
| -rw-r--r-- | src/H5Dvirtual.c | 439 |
1 files changed, 324 insertions, 115 deletions
diff --git a/src/H5Dvirtual.c b/src/H5Dvirtual.c index 3be2353..e07f538 100644 --- a/src/H5Dvirtual.c +++ b/src/H5Dvirtual.c @@ -35,6 +35,13 @@ * until the virtual dataset is closed. */ +/* + * Note: H5S_select_project_intersection has been updated to no longer require + * that the source and source intersect spaces have the same extent. This file + * should therefore be updated to remove code that ensures this condition, which + * should improve both maintainability and performance. + */ + /****************/ /* Module Setup */ /****************/ @@ -46,6 +53,7 @@ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ +#include "H5CXprivate.h" /* API Contexts */ #include "H5Dpkg.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5Fprivate.h" /* Files */ @@ -55,8 +63,9 @@ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ +#include "H5Pprivate.h" /* Property Lists */ #include "H5Sprivate.h" /* Dataspaces */ - +#include "H5VLprivate.h" /* Virtual Object Layer */ /****************/ /* Local Macros */ @@ -76,20 +85,20 @@ /********************/ /* 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, const H5S_t *file_space, const 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, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *fm); -static herr_t H5D__virtual_flush(H5D_t *dset, hid_t dxpl_id); +static herr_t H5D__virtual_flush(H5D_t *dset); /* Other functions */ static herr_t H5D__virtual_open_source_dset(const H5D_t *vdset, H5O_storage_virtual_ent_t *virtual_ent, - H5O_storage_virtual_srcdset_t *source_dset, hid_t dxpl_id); -static herr_t H5D__virtual_reset_source_dset( - H5O_storage_virtual_ent_t *virtual_ent, + H5O_storage_virtual_srcdset_t *source_dset); +static herr_t H5D__virtual_reset_source_dset(H5O_storage_virtual_ent_t *virtual_ent, H5O_storage_virtual_srcdset_t *source_dset); static herr_t H5D__virtual_str_append(const char *src, size_t src_len, char **p, char **buf, size_t *buf_size); @@ -98,7 +107,7 @@ static herr_t H5D__virtual_copy_parsed_name( static herr_t H5D__virtual_build_source_name(char *source_name, const H5O_storage_virtual_name_seg_t *parsed_name, size_t static_strlen, size_t nsubs, hsize_t blockno, char **built_name); -static herr_t H5D__virtual_init_all(const H5D_t *dset, hid_t dxpl_id); +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, const H5S_t *file_space, const H5S_t *mem_space, hsize_t *tot_nelmts); @@ -120,6 +129,7 @@ const H5D_layout_ops_t H5D_LOPS_VIRTUAL[1] = {{ NULL, H5D__virtual_init, H5D__virtual_is_space_alloc, + H5D__virtual_is_data_cached, NULL, H5D__virtual_read, H5D__virtual_write, @@ -146,7 +156,7 @@ H5FL_DEFINE(H5O_storage_virtual_name_seg_t); H5FL_DEFINE_STATIC(H5D_virtual_held_file_t); - + /*------------------------------------------------------------------------- * Function: H5D_virtual_check_mapping_pre * @@ -216,7 +226,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_virtual_check_mapping_pre() */ - + /*------------------------------------------------------------------------- * Function: H5D_virtual_check_mapping_post * @@ -284,7 +294,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_virtual_check_mapping_post() */ - + /*------------------------------------------------------------------------- * Function: H5D_virtual_update_min_dims * @@ -343,7 +353,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_virtual_update_min_dims() */ - + /*------------------------------------------------------------------------- * Function: H5D_virtual_check_min_dims * @@ -388,6 +398,144 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_virtual_check_min_dims() */ + +/*------------------------------------------------------------------------- + * Function: H5D__virtual_store_layout + * + * Purpose: Store virtual dataset layout information, for new dataset + * + * Note: We assume here that the contents of the heap block cannot + * change! If this ever stops being the case we must change + * this code to allow overwrites of the heap block. -NAF + * + * Return: Success: SUCCEED + * Failure: FAIL + * + * Programmer: Quincey Koziol + * Sunday, Feberuary 11, 2018 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout) +{ + uint8_t *heap_block = NULL; /* Block to add to heap */ + size_t *str_size = NULL; /* Array for VDS entry string lengths */ + uint8_t *heap_block_p; /* Pointer into the heap block, while encoding */ + size_t block_size; /* Total size of block needed */ + hsize_t tmp_nentries; /* Temp. variable for # of VDS entries */ + uint32_t chksum; /* Checksum for heap data */ + size_t i; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_PACKAGE + + /* Sanity checking */ + HDassert(f); + HDassert(layout); + HDassert(layout->storage.u.virt.serial_list_hobjid.addr == HADDR_UNDEF); + + /* Create block if # of used entries > 0 */ + if(layout->storage.u.virt.list_nused > 0) { + + /* Set the low/high bounds according to 'f' for the API context */ + H5CX_set_libver_bounds(f); + + /* Allocate array for caching results of strlen */ + if(NULL == (str_size = (size_t *)H5MM_malloc(2 * layout->storage.u.virt.list_nused * sizeof(size_t)))) + HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, FAIL, "unable to allocate string length array") + + /* + * Calculate heap block size + */ + + /* Version and number of entries */ + block_size = (size_t)1 + H5F_SIZEOF_SIZE(f); + + /* Calculate size of each entry */ + for(i = 0; i < layout->storage.u.virt.list_nused; i++) { + hssize_t select_serial_size; /* Size of serialized selection */ + + HDassert(layout->storage.u.virt.list[i].source_file_name); + HDassert(layout->storage.u.virt.list[i].source_dset_name); + HDassert(layout->storage.u.virt.list[i].source_select); + HDassert(layout->storage.u.virt.list[i].source_dset.virtual_select); + + /* Source file name */ + str_size[2 * i] = HDstrlen(layout->storage.u.virt.list[i].source_file_name) + (size_t)1; + block_size += str_size[2 * i]; + + /* Source dset name */ + str_size[(2 * i) + 1] = HDstrlen(layout->storage.u.virt.list[i].source_dset_name) + (size_t)1; + block_size += str_size[(2 * i) + 1]; + + /* Source selection */ + if((select_serial_size = H5S_SELECT_SERIAL_SIZE(layout->storage.u.virt.list[i].source_select)) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to check dataspace selection size") + block_size += (size_t)select_serial_size; + + /* Virtual dataset selection */ + if((select_serial_size = H5S_SELECT_SERIAL_SIZE(layout->storage.u.virt.list[i].source_dset.virtual_select)) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to check dataspace selection size") + block_size += (size_t)select_serial_size; + } /* end for */ + + /* Checksum */ + block_size += 4; + + + /* Allocate heap block */ + if(NULL == (heap_block = (uint8_t *)H5MM_malloc(block_size))) + HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, FAIL, "unable to allocate heap block") + + + /* + * Encode heap block + */ + heap_block_p = heap_block; + + /* Encode heap block encoding version */ + *heap_block_p++ = (uint8_t)H5O_LAYOUT_VDS_GH_ENC_VERS; + + /* Number of entries */ + tmp_nentries = (hsize_t)layout->storage.u.virt.list_nused; + H5F_ENCODE_LENGTH(f, heap_block_p, tmp_nentries) + + /* Encode each entry */ + for(i = 0; i < layout->storage.u.virt.list_nused; i++) { + /* Source file name */ + H5MM_memcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_file_name, str_size[2 * i]); + heap_block_p += str_size[2 * i]; + + /* Source dataset name */ + H5MM_memcpy((char *)heap_block_p, layout->storage.u.virt.list[i].source_dset_name, str_size[(2 * i) + 1]); + heap_block_p += str_size[(2 * i) + 1]; + + /* Source selection */ + if(H5S_SELECT_SERIALIZE(layout->storage.u.virt.list[i].source_select, &heap_block_p) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to serialize source selection") + + /* Virtual selection */ + if(H5S_SELECT_SERIALIZE(layout->storage.u.virt.list[i].source_dset.virtual_select, &heap_block_p) < 0) + HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to serialize virtual selection") + } /* end for */ + + /* Checksum */ + chksum = H5_checksum_metadata(heap_block, block_size - (size_t)4, 0); + UINT32ENCODE(heap_block_p, chksum) + + /* Insert block into global heap */ + if(H5HG_insert(f, block_size, heap_block, &(layout->storage.u.virt.serial_list_hobjid)) < 0) /* Casting away const OK --NAF */ + HGOTO_ERROR(H5E_OHDR, H5E_CANTINSERT, FAIL, "unable to insert virtual dataset heap block") + } /* end if */ + +done: + heap_block = (uint8_t *)H5MM_xfree(heap_block); + str_size = (size_t *)H5MM_xfree(str_size); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__virtual_store_layout() */ + /*------------------------------------------------------------------------- * Function: H5D__virtual_copy_layout @@ -552,7 +700,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_copy_layout() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_reset_layout * @@ -636,7 +784,7 @@ H5D__virtual_reset_layout(H5O_layout_t *layout) FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_reset_layout() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_copy * @@ -650,39 +798,36 @@ H5D__virtual_reset_layout(H5O_layout_t *layout) *------------------------------------------------------------------------- */ herr_t -H5D__virtual_copy(H5F_t H5_ATTR_UNUSED *f_dst, H5O_layout_t *layout_dst, - hid_t H5_ATTR_UNUSED dxpl_id) +H5D__virtual_copy(H5F_t *f_dst, H5O_layout_t *layout_dst) { herr_t ret_value = SUCCEED; -#ifdef NOT_YET FUNC_ENTER_PACKAGE -#endif /* NOT_YET */ - FUNC_ENTER_PACKAGE_NOERR #ifdef NOT_YET /* Check for copy to the same file */ if(f_dst == f_src) { /* Increase reference count on global heap object */ - if((heap_rc = H5HG_link(f_dst, dxpl_id, (H5HG_t *)&(layout_dst->u.virt.serial_list_hobjid), 1)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTMODIFY, FAIL, "unable to adjust global heap refence count") + if((heap_rc = H5HG_link(f_dst, (H5HG_t *)&(layout_dst->u.virt.serial_list_hobjid), 1)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTMODIFY, FAIL, "unable to adjust global heap reference count") } /* end if */ else #endif /* NOT_YET */ { - /* Reset global heap id so a new heap object is created when the message - * is flushed */ + /* Reset global heap id */ layout_dst->storage.u.virt.serial_list_hobjid.addr = HADDR_UNDEF; layout_dst->storage.u.virt.serial_list_hobjid.idx = (size_t)0; + + /* Write the VDS data to destination file's heap */ + if(H5D__virtual_store_layout(f_dst, layout_dst) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to store VDS info") } /* end block/else */ -#ifdef NOT_YET done: -#endif /* NOT_YET */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_copy() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_delete * @@ -696,7 +841,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__virtual_delete(H5F_t *f, hid_t dxpl_id, H5O_storage_t *storage) +H5D__virtual_delete(H5F_t *f, H5O_storage_t *storage) { #ifdef NOT_YET int heap_rc; /* Reference count of global heap object */ @@ -714,12 +859,12 @@ H5D__virtual_delete(H5F_t *f, hid_t dxpl_id, H5O_storage_t *storage) if(storage->u.virt.serial_list_hobjid.addr != HADDR_UNDEF) { #ifdef NOT_YET /* Unlink the global heap block */ - if((heap_rc = H5HG_link(f, dxpl_id, (H5HG_t *)&(storage->u.virt.serial_list_hobjid), -1)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTMODIFY, FAIL, "unable to adjust global heap refence count") + if((heap_rc = H5HG_link(f, (H5HG_t *)&(storage->u.virt.serial_list_hobjid), -1)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTMODIFY, FAIL, "unable to adjust global heap reference count") if(heap_rc == 0) #endif /* NOT_YET */ /* Delete the global heap block */ - if(H5HG_remove(f, dxpl_id, (H5HG_t *)&(storage->u.virt.serial_list_hobjid)) < 0) + if(H5HG_remove(f, (H5HG_t *)&(storage->u.virt.serial_list_hobjid)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to remove heap object") } /* end if */ @@ -731,7 +876,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_delete */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_open_source_dset * @@ -747,11 +892,10 @@ done: static herr_t H5D__virtual_open_source_dset(const H5D_t *vdset, H5O_storage_virtual_ent_t *virtual_ent, - H5O_storage_virtual_srcdset_t *source_dset, hid_t dxpl_id) + H5O_storage_virtual_srcdset_t *source_dset) { H5F_t *src_file = NULL; /* Source file */ hbool_t src_file_open = FALSE; /* Whether we have opened and need to close src_file */ - H5G_loc_t src_root_loc; /* Object location of source file root group */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -765,28 +909,42 @@ H5D__virtual_open_source_dset(const H5D_t *vdset, /* Check if we need to open the source file */ if(HDstrcmp(source_dset->file_name, ".")) { - /* Open the source file */ - if(NULL == (src_file = H5F_open(source_dset->file_name, H5F_INTENT(vdset->oloc.file) & (H5F_ACC_RDWR | H5F_ACC_SWMR_WRITE | H5F_ACC_SWMR_READ), H5P_FILE_CREATE_DEFAULT, vdset->shared->layout.storage.u.virt.source_fapl, dxpl_id))) - H5E_clear_stack(NULL); /* Quick hack until proper support for H5Fopen with missing file is implemented */ - else + unsigned intent; /* File access permissions */ + + /* Get the virtual dataset's file open flags ("intent") */ + intent = H5F_INTENT(vdset->oloc.file); + + /* Try opening the file */ + src_file = H5F_prefix_open_file(vdset->oloc.file, H5F_PREFIX_VDS, vdset->shared->vds_prefix, source_dset->file_name, intent, vdset->shared->layout.storage.u.virt.source_fapl); + + /* If we opened the source file here, we should close it when leaving */ + if(src_file) src_file_open = TRUE; + else + /* Reset the error stack */ + H5E_clear_stack(NULL); } /* end if */ else /* Source file is ".", use the virtual dataset's file */ src_file = vdset->oloc.file; if(src_file) { + H5G_loc_t src_root_loc; /* Object location of source file root group */ + /* Set up the root group in the destination file */ if(NULL == (src_root_loc.oloc = H5G_oloc(H5G_rootof(src_file)))) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "unable to get object location for root group") if(NULL == (src_root_loc.path = H5G_nameof(H5G_rootof(src_file)))) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "unable to get path for root group") - /* Open the source dataset */ - if(NULL == (source_dset->dset = H5D__open_name(&src_root_loc, source_dset->dset_name, vdset->shared->layout.storage.u.virt.source_dapl, dxpl_id))) { - H5E_clear_stack(NULL); /* Quick hack until proper support for H5Dopen with missing file is implemented */ + /* Try opening the source dataset */ + source_dset->dset = H5D__open_name(&src_root_loc, source_dset->dset_name, vdset->shared->layout.storage.u.virt.source_dapl); + + /* Dataset does not exist */ + if(NULL == source_dset->dset) { + /* Reset the error stack */ + H5E_clear_stack(NULL); - /* Dataset does not exist */ source_dset->dset_exists = FALSE; } /* end if */ else { @@ -803,15 +961,15 @@ H5D__virtual_open_source_dset(const H5D_t *vdset, } /* end if */ done: - /* Close source file */ + /* Release resources */ if(src_file_open) - if(H5F_try_close(src_file, NULL) < 0) + if(H5F_efc_close(vdset->oloc.file, src_file) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEFILE, FAIL, "can't close source file") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_open_source_dset() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_reset_source_dset * @@ -898,7 +1056,7 @@ H5D__virtual_reset_source_dset(H5O_storage_virtual_ent_t *virtual_ent, FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_reset_source_dset() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_str_append * @@ -962,7 +1120,7 @@ H5D__virtual_str_append(const char *src, size_t src_len, char **p, char **buf, /* Copy string to *p. Note that since src in not NULL terminated, we must * use memcpy */ - (void)HDmemcpy(*p, src, src_len); + H5MM_memcpy(*p, src, src_len); /* Advance *p */ *p += src_len; @@ -974,7 +1132,7 @@ done: FUNC_LEAVE_NOAPI(ret_value); } /* end H5D__virtual_str_append() */ - + /*------------------------------------------------------------------------- * Function: H5D_virtual_parse_source_name * @@ -1090,7 +1248,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_virtual_parse_source_name() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_copy_parsed_name * @@ -1147,7 +1305,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_copy_parsed_name() */ - + /*------------------------------------------------------------------------- * Function: H5D_virtual_free_parsed_name * @@ -1180,7 +1338,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_virtual_free_parsed_name() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_build_source_name * @@ -1282,7 +1440,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_build_source_name() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_set_extent_unlim * @@ -1299,7 +1457,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__virtual_set_extent_unlim(const H5D_t *dset, hid_t dxpl_id) +H5D__virtual_set_extent_unlim(const H5D_t *dset) { H5O_storage_virtual_t *storage; hsize_t new_dims[H5S_MAX_RANK]; @@ -1335,7 +1493,7 @@ H5D__virtual_set_extent_unlim(const H5D_t *dset, hid_t dxpl_id) /* Non-printf mapping */ /* Open source dataset */ if(!storage->list[i].source_dset.dset) - if(H5D__virtual_open_source_dset(dset, &storage->list[i], &storage->list[i].source_dset, dxpl_id) < 0) + 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") /* Check if source dataset is open */ @@ -1407,7 +1565,7 @@ H5D__virtual_set_extent_unlim(const H5D_t *dset, hid_t dxpl_id) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "failed to clip unlimited selection") } /* end if */ - /* Update cached values unlim_extent_source and + /* Update cached values unlim_extent_source and * clip_size_virtual */ storage->list[i].unlim_extent_source = curr_dims[storage->list[i].unlim_dim_source]; storage->list[i].clip_size_virtual = clip_size; @@ -1473,7 +1631,7 @@ H5D__virtual_set_extent_unlim(const H5D_t *dset, hid_t dxpl_id) storage->list[i].sub_dset[j].clipped_virtual_select = storage->list[i].sub_dset[j].virtual_select; /* Open source dataset */ - if(H5D__virtual_open_source_dset(dset, &storage->list[i], &storage->list[i].sub_dset[j], dxpl_id) < 0) + 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") if(storage->list[i].sub_dset[j].dset) { @@ -1556,11 +1714,11 @@ H5D__virtual_set_extent_unlim(const H5D_t *dset, hid_t dxpl_id) if(changed) { /* Update VDS extent */ if(H5S_set_extent(dset->shared->space, new_dims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") /* Mark the space as dirty, for later writing to the file */ - if(H5F_INTENT(dset->oloc.file) & H5F_ACC_RDWR) - if(H5D__mark(dset, dxpl_id, H5D_MARK_SPACE) < 0) + if(H5F_INTENT(dset->oloc.file) & H5F_ACC_RDWR) + if(H5D__mark(dset, H5D_MARK_SPACE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to mark dataspace as dirty") } /* end if */ @@ -1679,24 +1837,24 @@ H5D__virtual_set_extent_unlim(const H5D_t *dset, hid_t dxpl_id) /* Update top level virtual_select and clipped_virtual_select * extents */ if(H5S_set_extent(storage->list[i].source_dset.virtual_select, new_dims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") if((storage->list[i].source_dset.clipped_virtual_select != storage->list[i].source_dset.virtual_select) && storage->list[i].source_dset.clipped_virtual_select) if(H5S_set_extent(storage->list[i].source_dset.clipped_virtual_select, new_dims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") /* Update sub dataset virtual_select and clipped_virtual_select * extents */ for(j = 0; j < storage->list[i].sub_dset_nalloc; j++) if(storage->list[i].sub_dset[j].virtual_select) { if(H5S_set_extent(storage->list[i].sub_dset[j].virtual_select, new_dims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") if((storage->list[i].sub_dset[j].clipped_virtual_select != storage->list[i].sub_dset[j].virtual_select) && storage->list[i].sub_dset[j].clipped_virtual_select) if(H5S_set_extent(storage->list[i].sub_dset[j].clipped_virtual_select, new_dims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") } /* end if */ else HDassert(!storage->list[i].sub_dset[j].clipped_virtual_select); @@ -1710,7 +1868,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_set_extent_unlim() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_init_all * @@ -1727,7 +1885,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__virtual_init_all(const H5D_t *dset, hid_t dxpl_id) +H5D__virtual_init_all(const H5D_t *dset) { H5O_storage_virtual_t *storage; hsize_t virtual_dims[H5S_MAX_RANK]; @@ -1757,7 +1915,7 @@ H5D__virtual_init_all(const H5D_t *dset, hid_t dxpl_id) /* Non-printf mapping */ /* Open source dataset */ if(!storage->list[i].source_dset.dset) - if(H5D__virtual_open_source_dset(dset, &storage->list[i], &storage->list[i].source_dset, dxpl_id) < 0) + 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") /* Check if source dataset is open */ @@ -1934,7 +2092,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_init_all() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_init * @@ -1949,8 +2107,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__virtual_init(H5F_t *f, hid_t H5_ATTR_UNUSED dxpl_id, const H5D_t *dset, - hid_t dapl_id) +H5D__virtual_init(H5F_t *f, const H5D_t *dset, hid_t dapl_id) { H5O_storage_virtual_t *storage; /* Convenience pointer */ H5P_genplist_t *dapl; /* Data access property list object pointer */ @@ -2029,7 +2186,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_init() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_is_space_alloc * @@ -2061,7 +2218,55 @@ H5D__virtual_is_space_alloc(const H5O_storage_t H5_ATTR_UNUSED *storage) FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_is_space_alloc() */ - + +/*------------------------------------------------------------------------- + * Function: H5D__virtual_is_data_cached + * + * Purpose: Query if raw data is cached for dataset + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner + * Wednessday, March 6, 2016 + * + *------------------------------------------------------------------------- + */ +static hbool_t +H5D__virtual_is_data_cached(const H5D_shared_t *shared_dset) +{ + const H5O_storage_virtual_t *storage; /* Convenience pointer */ + size_t i, j; /* Local index variables */ + hbool_t ret_value = FALSE; /* Return value */ + + FUNC_ENTER_PACKAGE_NOERR + + /* Sanity checks */ + HDassert(shared_dset); + storage = &shared_dset->layout.storage.u.virt; + + /* Iterate over mappings */ + for(i = 0; i < storage->list_nused; i++) + /* Check for "printf" source dataset resolution */ + 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++) + /* Check for cahced data in source dset */ + if(storage->list[i].sub_dset[j].dset + && storage->list[i].sub_dset[j].dset->shared->layout.ops->is_data_cached + && storage->list[i].sub_dset[j].dset->shared->layout.ops->is_data_cached(storage->list[i].sub_dset[j].dset->shared)) + HGOTO_DONE(TRUE); + } /* end if */ + else + if(storage->list[i].source_dset.dset + && storage->list[i].source_dset.dset->shared->layout.ops->is_data_cached + && storage->list[i].source_dset.dset->shared->layout.ops->is_data_cached(storage->list[i].source_dset.dset->shared)) + HGOTO_DONE(TRUE); + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D__virtual_is_data_cached() */ + + /*------------------------------------------------------------------------- * Function: H5D__virtual_pre_io * @@ -2100,7 +2305,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, /* Initialize layout if necessary */ if(!storage->init) - if(H5D__virtual_init_all(io_info->dset, io_info->md_dxpl_id) < 0) + if(H5D__virtual_init_all(io_info->dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize virtual layout") /* Initialize tot_nelmts */ @@ -2158,7 +2363,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, * 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], &storage->list[i].sub_dset[j], io_info->md_dxpl_id) < 0) + if(H5D__virtual_open_source_dset(io_info->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 */ @@ -2183,7 +2388,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, /* Temporarily set extent of virtual selection to bounds */ if(H5S_set_extent(storage->list[i].sub_dset[j].virtual_select, vbounds_end) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + 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) @@ -2201,15 +2406,15 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, /* Project intersection of virtual space and clipped * virtual space onto source space (create * clipped_source_select) */ - if(H5S_select_project_intersection(storage->list[i].sub_dset[j].virtual_select, storage->list[i].source_select, storage->list[i].sub_dset[j].clipped_virtual_select, &storage->list[i].sub_dset[j].clipped_source_select) < 0) + if(H5S_select_project_intersection(storage->list[i].sub_dset[j].virtual_select, storage->list[i].source_select, storage->list[i].sub_dset[j].clipped_virtual_select, &storage->list[i].sub_dset[j].clipped_source_select, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto memory space") /* Set extents of virtual_select and * clipped_virtual_select to virtual extent */ if(H5S_set_extent(storage->list[i].sub_dset[j].virtual_select, tmp_dims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") if(H5S_set_extent(storage->list[i].sub_dset[j].clipped_virtual_select, tmp_dims) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of dataspace") } /* end if */ } /* end if */ @@ -2218,7 +2423,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, if(storage->list[i].sub_dset[j].clipped_virtual_select) { /* Project intersection of file space and mapping virtual space * onto memory space */ - if(H5S_select_project_intersection(file_space, mem_space, storage->list[i].sub_dset[j].clipped_virtual_select, &storage->list[i].sub_dset[j].projected_mem_space) < 0) + if(H5S_select_project_intersection(file_space, mem_space, storage->list[i].sub_dset[j].clipped_virtual_select, &storage->list[i].sub_dset[j].projected_mem_space, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto memory space") /* Check number of elements selected */ @@ -2230,7 +2435,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, /* 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], &storage->list[i].sub_dset[j], io_info->md_dxpl_id) < 0) + if(H5D__virtual_open_source_dset(io_info->dset, &storage->list[i], &storage->list[i].sub_dset[j]) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open source dataset") /* If the source dataset is not open, mark the selected @@ -2246,7 +2451,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close projected memory space") storage->list[i].sub_dset[j].projected_mem_space = NULL; } /* end if */ - else + else *tot_nelmts += (hsize_t)select_nelmts; } /* end if */ } /* end for */ @@ -2255,7 +2460,7 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, if(storage->list[i].source_dset.clipped_virtual_select) { /* Project intersection of file space and mapping virtual space onto * memory space */ - if(H5S_select_project_intersection(file_space, mem_space, storage->list[i].source_dset.clipped_virtual_select, &storage->list[i].source_dset.projected_mem_space) < 0) + if(H5S_select_project_intersection(file_space, mem_space, storage->list[i].source_dset.clipped_virtual_select, &storage->list[i].source_dset.projected_mem_space, TRUE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto memory space") /* Check number of elements selected, add to tot_nelmts */ @@ -2265,9 +2470,9 @@ H5D__virtual_pre_io(H5D_io_info_t *io_info, /* Check if anything is selected */ if(select_nelmts > (hssize_t)0) { /* Open source dataset */ - if(!storage->list[i].source_dset.dset) + if(!storage->list[i].source_dset.dset) /* Try to open dataset */ - if(H5D__virtual_open_source_dset(io_info->dset, &storage->list[i], &storage->list[i].source_dset, io_info->md_dxpl_id) < 0) + if(H5D__virtual_open_source_dset(io_info->dset, &storage->list[i], &storage->list[i].source_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open source dataset") /* If the source dataset is not open, mark the selected elements @@ -2302,7 +2507,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_pre_io() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_post_io * @@ -2352,7 +2557,7 @@ H5D__virtual_post_io(H5O_storage_virtual_t *storage) FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_post_io() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_read_one * @@ -2385,11 +2590,11 @@ 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, &projected_src_space) < 0) + if(H5S_select_project_intersection(source_dset->clipped_virtual_select, source_dset->clipped_source_select, 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->raw_dxpl_id, io_info->u.rbuf) < 0) + 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") /* Close projected_src_space */ @@ -2409,7 +2614,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_read_one() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_read * @@ -2506,8 +2711,7 @@ H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, 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, io_info->md_dxpl_id) < 0) + 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) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "filling buf failed") #ifndef NDEBUG @@ -2542,7 +2746,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_read() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_write_one * @@ -2577,11 +2781,11 @@ H5D__virtual_write_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, * extent in the unlimited dimension. -NAF */ /* Project intersection of file space and mapping virtual space onto * mapping source space */ - if(H5S_select_project_intersection(source_dset->virtual_select, source_dset->clipped_source_select, file_space, &projected_src_space) < 0) + if(H5S_select_project_intersection(source_dset->virtual_select, source_dset->clipped_source_select, 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->raw_dxpl_id, io_info->u.wbuf) < 0) + 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") /* Close projected_src_space */ @@ -2601,7 +2805,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_write_one() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_write * @@ -2678,7 +2882,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_write() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_flush * @@ -2692,7 +2896,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__virtual_flush(H5D_t *dset, hid_t dxpl_id) +H5D__virtual_flush(H5D_t *dset) { H5O_storage_virtual_t *storage; /* Convenient pointer into layout struct */ size_t i, j; /* Local index variables */ @@ -2713,20 +2917,20 @@ H5D__virtual_flush(H5D_t *dset, hid_t dxpl_id) for(j = 0; j < storage->list[i].sub_dset_nused; j++) if(storage->list[i].sub_dset[j].dset) /* Flush source dataset */ - if(H5D__flush_real(storage->list[i].sub_dset[j].dset, dxpl_id) < 0) + if(H5D__flush_real(storage->list[i].sub_dset[j].dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to flush source dataset") } /* end if */ else if(storage->list[i].source_dset.dset) /* Flush source dataset */ - if(H5D__flush_real(storage->list[i].source_dset.dset, dxpl_id) < 0) + if(H5D__flush_real(storage->list[i].source_dset.dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to flush source dataset") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_flush() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_hold_source_dset_files * @@ -2794,17 +2998,15 @@ H5D__virtual_hold_source_dset_files(const H5D_t *dset, H5D_virtual_held_file_t * } /* end if */ done: - if(ret_value < 0) { + if(ret_value < 0) /* Release hold on files and delete list on error */ - if(*head) - if(H5D__virtual_release_source_dset_files(*head) < 0) - HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release source datasets' files held open") - } /* end if */ + if(*head && H5D__virtual_release_source_dset_files(*head) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release source datasets' files held open") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_hold_source_dset_files() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_refresh_source_dset * @@ -2818,10 +3020,11 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__virtual_refresh_source_dset(H5D_t **dset, hid_t dxpl_id) +H5D__virtual_refresh_source_dset(H5D_t **dset) { - hid_t dset_id; /* Temporary dataset identifier */ - herr_t ret_value = SUCCEED; /* Return value */ + hid_t temp_id = H5I_INVALID_HID; /* Temporary dataset identifier */ + H5VL_object_t *vol_obj = NULL; /* VOL object stored with the ID */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -2829,22 +3032,28 @@ H5D__virtual_refresh_source_dset(H5D_t **dset, hid_t dxpl_id) HDassert(dset && *dset); /* Get a temporary identifier for this source dataset */ - if((dset_id = H5I_register(H5I_DATASET, *dset, FALSE)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register source dataset ID") + if((temp_id = H5VL_wrap_register(H5I_DATASET, *dset, FALSE)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register (temporary) source dataset ID") /* Refresh source dataset */ - if(H5D__refresh(dset_id, *dset, dxpl_id) < 0) + if(H5D__refresh(temp_id, *dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to refresh source dataset") /* Discard the identifier & replace the dataset */ - if(NULL == (*dset = (H5D_t *)H5I_remove(dset_id))) + if(NULL == (vol_obj = (H5VL_object_t *)H5I_remove(temp_id))) HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "can't unregister source dataset ID") + if(NULL == (*dset = (H5D_t *)H5VL_object_unwrap(vol_obj))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve library object from VOL object") + vol_obj->data = NULL; done: + if(vol_obj && H5VL_free_object(vol_obj) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "unable to free VOL object") + FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__virtual_refresh_source_dsets() */ +} /* end H5D__virtual_refresh_source_dset() */ + - /*------------------------------------------------------------------------- * Function: H5D__virtual_refresh_source_dsets * @@ -2858,7 +3067,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__virtual_refresh_source_dsets(H5D_t *dset, hid_t dxpl_id) +H5D__virtual_refresh_source_dsets(H5D_t *dset) { H5O_storage_virtual_t *storage; /* Convenient pointer into layout struct */ size_t i; /* Local index variable */ @@ -2883,21 +3092,21 @@ H5D__virtual_refresh_source_dsets(H5D_t *dset, hid_t dxpl_id) /* Check if sub-source dataset is open */ if(storage->list[i].sub_dset[j].dset) /* Refresh sub-source dataset */ - if(H5D__virtual_refresh_source_dset(&storage->list[i].sub_dset[j].dset, dxpl_id) < 0) + if(H5D__virtual_refresh_source_dset(&storage->list[i].sub_dset[j].dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to refresh source dataset") } /* end if */ else /* Check if source dataset is open */ if(storage->list[i].source_dset.dset) /* Refresh source dataset */ - if(H5D__virtual_refresh_source_dset(&storage->list[i].source_dset.dset, dxpl_id) < 0) + if(H5D__virtual_refresh_source_dset(&storage->list[i].source_dset.dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to refresh source dataset") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_refresh_source_dsets() */ - + /*------------------------------------------------------------------------- * Function: H5D__virtual_release_source_dset_files * |