/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Programmer: Neil Fortner * Wednesday, January 28, 2015 * * Purpose: * VDSINC */ /****************/ /* Module Setup */ /****************/ #define H5D_PACKAGE /* Suppress error about including H5Dpkg */ /***********/ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ #include "H5Dpkg.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5Fprivate.h" /* Files */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Gprivate.h" /* Groups */ #include "H5HGprivate.h" /* Global Heaps */ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Sprivate.h" /* Dataspaces */ /****************/ /* Local Macros */ /****************/ /* Default size for sub_dset array */ #define H5D_VIRTUAL_DEF_SUB_DSET_SIZE 128 /******************/ /* Local Typedefs */ /******************/ /********************/ /* Local Prototypes */ /********************/ /* Layout operation callbacks */ 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); /* 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_str_append(const char *src, size_t src_len, char **p, char **buf, size_t *buf_size); static herr_t H5D__virtual_copy_parsed_name( H5O_storage_virtual_name_seg_t **dst, H5O_storage_virtual_name_seg_t *src); 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_read_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, const 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, const H5S_t *file_space, H5O_storage_virtual_srcdset_t *source_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); static herr_t H5D__virtual_post_io(H5O_storage_virtual_t *storage); /*********************/ /* Package Variables */ /*********************/ /* Contiguous storage layout I/O ops */ const H5D_layout_ops_t H5D_LOPS_VIRTUAL[1] = {{ NULL, H5D__virtual_init, H5D__virtual_is_space_alloc, NULL, H5D__virtual_read, H5D__virtual_write, #ifdef H5_HAVE_PARALLEL H5D__virtual_collective_read, //VDSINC H5D__virtual_collective_write, //VDSINC #endif /* H5_HAVE_PARALLEL */ NULL, NULL, H5D__virtual_flush, NULL }}; /*******************/ /* Local Variables */ /*******************/ /* Declare a free list to manage the H5O_storage_virtual_name_seg_t struct */ H5FL_DEFINE(H5O_storage_virtual_name_seg_t); /*------------------------------------------------------------------------- * Function: H5D_virtual_update_min_dims * * Purpose: Updates the virtual layout's "min_dims" field to take into * account the "idx"th entry in the mapping list. The entry * must be complete, though top level fields list_nused does * (and of course min_dims) do not need to take it into * account. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * February 10, 2015 * *------------------------------------------------------------------------- */ herr_t H5D_virtual_update_min_dims(H5O_layout_t *layout, size_t idx) { H5S_sel_type sel_type; int rank; hsize_t bounds_start[H5S_MAX_RANK]; hsize_t bounds_end[H5S_MAX_RANK]; int i; herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI(FAIL) HDassert(layout); HDassert(layout->type == H5D_VIRTUAL); HDassert(idx < layout->storage.u.virt.list_nalloc); /* Get type of selection */ if(H5S_SEL_ERROR == (sel_type = H5S_GET_SELECT_TYPE(layout->storage.u.virt.list[idx].source_dset.virtual_select))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get selection type") /* Do not update min_dims for "all" or "none" selections */ if((sel_type == H5S_SEL_ALL) || (sel_type == H5S_SEL_NONE)) HGOTO_DONE(SUCCEED) /* Get rank of vspace */ if((rank = H5S_GET_EXTENT_NDIMS(layout->storage.u.virt.list[idx].source_dset.virtual_select)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get number of dimensions") /* Get selection bounds */ if(H5S_SELECT_BOUNDS(layout->storage.u.virt.list[idx].source_dset.virtual_select, bounds_start, bounds_end) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get selection bounds") /* Update min_dims */ for(i = 0; i < rank; i++) /* Don't check unlimited dimensions in the selection */ if((i != layout->storage.u.virt.list[idx].unlim_dim_virtual) && (bounds_end[i] >= layout->storage.u.virt.min_dims[i])) layout->storage.u.virt.min_dims[i] = bounds_end[i] + (hsize_t)1; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_virtual_update_min_dims() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_copy_layout * * Purpose: Deep copies virtual storage layout message in memory. * This function assumes that the top-level struct has * already been copied (so the source struct retains * ownership of the fields passed to this function). * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * February 10, 2015 * *------------------------------------------------------------------------- */ herr_t H5D__virtual_copy_layout(H5O_layout_t *layout) { H5O_storage_virtual_ent_t *orig_list = NULL; size_t i; herr_t ret_value = SUCCEED; FUNC_ENTER_PACKAGE HDassert(layout); HDassert(layout->type == H5D_VIRTUAL); if(layout->storage.u.virt.list_nused > 0) { HDassert(layout->storage.u.virt.list); /* Save original entry list for use as the "source" */ orig_list = layout->storage.u.virt.list; /* Allocate memory for the list */ if(NULL == (layout->storage.u.virt.list = (H5O_storage_virtual_ent_t *)H5MM_calloc(layout->storage.u.virt.list_nused * sizeof(H5O_storage_virtual_ent_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate memory for virtual dataset entry list") layout->storage.u.virt.list_nalloc = layout->storage.u.virt.list_nused; /* Copy the list entries, though set source_dset.dset and sub_dset to * NULL */ for(i = 0; i < layout->storage.u.virt.list_nused; i++) { if(NULL == (layout->storage.u.virt.list[i].source_dset.file_name = HDstrdup(orig_list[i].source_dset.file_name))) HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source file name") if(NULL == (layout->storage.u.virt.list[i].source_dset.dset_name = HDstrdup(orig_list[i].source_dset.dset_name))) HGOTO_ERROR(H5E_DATASET, H5E_RESOURCE, FAIL, "unable to duplicate source dataset name") if(NULL == (layout->storage.u.virt.list[i].source_dset.virtual_select = H5S_copy(orig_list[i].source_dset.virtual_select, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy virtual selection") if(NULL == (layout->storage.u.virt.list[i].source_select = H5S_copy(orig_list[i].source_select, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy source selection") if(orig_list[i].unlim_dim_virtual < 0) { layout->storage.u.virt.list[i].source_dset.clipped_source_select = layout->storage.u.virt.list[i].source_select; layout->storage.u.virt.list[i].source_dset.clipped_virtual_select = layout->storage.u.virt.list[i].source_dset.virtual_select; } /* end if */ if(H5D__virtual_copy_parsed_name(&layout->storage.u.virt.list[i].parsed_source_file_name, orig_list[i].parsed_source_file_name) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy parsed source file name") layout->storage.u.virt.list[i].psfn_static_strlen = orig_list[i].psfn_static_strlen; layout->storage.u.virt.list[i].psfn_nsubs = orig_list[i].psfn_nsubs; if(H5D__virtual_copy_parsed_name(&layout->storage.u.virt.list[i].parsed_source_dset_name, orig_list[i].parsed_source_dset_name) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy parsed source dataset name") layout->storage.u.virt.list[i].psdn_static_strlen = orig_list[i].psdn_static_strlen; layout->storage.u.virt.list[i].psdn_nsubs = orig_list[i].psdn_nsubs; layout->storage.u.virt.list[i].unlim_dim_source = orig_list[i].unlim_dim_source; layout->storage.u.virt.list[i].unlim_dim_virtual = orig_list[i].unlim_dim_virtual; layout->storage.u.virt.list[i].unlim_extent_source = orig_list[i].unlim_extent_source; layout->storage.u.virt.list[i].unlim_extent_virtual = orig_list[i].unlim_extent_virtual; layout->storage.u.virt.list[i].clip_size_source = orig_list[i].clip_size_source; layout->storage.u.virt.list[i].clip_size_virtual = orig_list[i].clip_size_virtual; layout->storage.u.virt.list[i].source_space_status = orig_list[i].source_space_status; layout->storage.u.virt.list[i].virtual_space_status = orig_list[i].virtual_space_status; } /* end for */ } /* end if */ else { HDassert(0 && "checking code coverage...");//VDSINC /* Zero out other fields related to list, just to be sure */ layout->storage.u.virt.list = NULL; layout->storage.u.virt.list_nalloc = 0; } /* end else */ /* New layout is not fully initialized */ layout->storage.u.virt.init = FALSE; done: /* Release allocated resources on failure */ if((ret_value < 0) && orig_list && (orig_list != layout->storage.u.virt.list)) if(H5D__virtual_reset_layout(layout) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset virtual layout") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_copy_layout() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_reset_layout * * Purpose: Frees internal structures in a virtual storage layout * message in memory. This function is safe to use on * incomplete structures (for recovery from failure) provided * the internal structures are initialized with all bytes set * to 0. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * February 11, 2015 * *------------------------------------------------------------------------- */ herr_t H5D__virtual_reset_layout(H5O_layout_t *layout) { size_t i, j; herr_t ret_value = SUCCEED; FUNC_ENTER_PACKAGE HDassert(layout); HDassert(layout->type == H5D_VIRTUAL); /* Free the list entries. Note we always attempt to free everything even in * the case of a failure. Because of this, and because we free the list * afterwards, we do not need to zero out the memory in the list. */ for(i = 0; i < layout->storage.u.virt.list_nused; i++) { /* Free source_dset */ if(H5D__virtual_reset_source_dset(&layout->storage.u.virt.list[i], &layout->storage.u.virt.list[i].source_dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset source dataset") /* Free sub_dset */ for(j = 0; j < layout->storage.u.virt.list[i].sub_dset_nalloc; j++) if(H5D__virtual_reset_source_dset(&layout->storage.u.virt.list[i], &layout->storage.u.virt.list[i].sub_dset[j]) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset source dataset") layout->storage.u.virt.list[i].sub_dset = (H5O_storage_virtual_srcdset_t *)H5MM_xfree(layout->storage.u.virt.list[i].sub_dset); /* Free source_select */ if(layout->storage.u.virt.list[i].source_select) if(H5S_close(layout->storage.u.virt.list[i].source_select) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release source selection") /* Free parsed_source_file_name */ H5D_virtual_free_parsed_name(layout->storage.u.virt.list[i].parsed_source_file_name); /* Free parsed_source_dset_name */ H5D_virtual_free_parsed_name(layout->storage.u.virt.list[i].parsed_source_dset_name); } /* end for */ /* Free the list */ layout->storage.u.virt.list = (H5O_storage_virtual_ent_t *)H5MM_xfree(layout->storage.u.virt.list); layout->storage.u.virt.list_nalloc = (size_t)0; layout->storage.u.virt.list_nused = (size_t)0; (void)HDmemset(layout->storage.u.virt.min_dims, 0, sizeof(layout->storage.u.virt.min_dims)); /* The list is no longer initialized */ layout->storage.u.virt.init = FALSE; /* Note the lack of a done: label. This is because there are no HGOTO_ERROR * calls. If one is added, a done: label must also be added */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_reset_layout() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_delete * * Purpose: Delete the file space for a virtual dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * February 6, 2015 * *------------------------------------------------------------------------- */ herr_t H5D__virtual_delete(H5F_t *f, hid_t dxpl_id, H5O_storage_t *storage) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* check args */ HDassert(f); HDassert(storage); HDassert(storage->type == H5D_VIRTUAL); /* Delete the global heap block */ if(H5HG_remove(f, dxpl_id, (H5HG_t *)&(storage->u.virt.serial_list_hobjid)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "Unable to remove heap object") /* Clear global heap ID in storage */ storage->u.virt.serial_list_hobjid.addr = HADDR_UNDEF; storage->u.virt.serial_list_hobjid.idx = 0; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_delete */ /*------------------------------------------------------------------------- * Function: H5D__virtual_open_source_dset * * Purpose: Attempts to open a source dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * March 6, 2015 * *------------------------------------------------------------------------- */ 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) { 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 /* Sanity check */ HDassert(vdset); HDassert(source_dset); HDassert(!source_dset->dset); HDassert(source_dset->file_name); HDassert(source_dset->dset_name); /* Get dapl and fapl from current (virtual dataset) location? VDSINC */ /* Write code to check if these exist and return without opening dset * otherwise VDSINC */ /* 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, H5P_FILE_CREATE_DEFAULT, H5P_FILE_ACCESS_DEFAULT, dxpl_id))) H5E_clear_stack(NULL); //Quick hack until proper support for H5Fopen with missing file is implemented VDSINC HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENFILE, FAIL, "unable to open source file") else src_file_open = TRUE; } /* end if */ else /* Source file is ".", use the virtual dataset's file */ src_file = vdset->oloc.file; if(src_file) { /* 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, H5P_DATASET_ACCESS_DEFAULT, dxpl_id))) H5E_clear_stack(NULL); //Quick hack until proper support for H5Fopen with missing file is implemented VDSINC HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open dataset") else /* Patch the source selection if necessary */ if(virtual_ent->source_space_status != H5O_VIRTUAL_STATUS_CORRECT) { if(H5S_extent_copy(virtual_ent->source_select, source_dset->dset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy source dataspace extent") virtual_ent->source_space_status = H5O_VIRTUAL_STATUS_CORRECT; } /* end if */ } /* end if */ done: /* Close source file */ if(src_file_open) if(H5F_try_close(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 * * Purpose: Frees space reference by a source dataset struct. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * May 20, 2015 * *------------------------------------------------------------------------- */ static herr_t H5D__virtual_reset_source_dset(H5O_storage_virtual_ent_t *virtual_ent, H5O_storage_virtual_srcdset_t *source_dset) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(source_dset); /* Free dataset */ if(source_dset->dset) { if(H5D_close(source_dset->dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to close source dataset") source_dset->dset = NULL; } /* end if */ /* Free file name */ if((source_dset == &virtual_ent->source_dset) || virtual_ent->parsed_source_file_name) source_dset->file_name = (char *)H5MM_xfree(source_dset->file_name); /* Free dataset name */ if((source_dset == &virtual_ent->source_dset) || virtual_ent->parsed_source_dset_name) source_dset->dset_name = (char *)H5MM_xfree(source_dset->dset_name); /* Free clipped virtual selection */ if(source_dset->clipped_virtual_select) { if(source_dset->clipped_virtual_select != source_dset->virtual_select) if(H5S_close(source_dset->clipped_virtual_select) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release clipped virtual selection") source_dset->clipped_virtual_select = NULL; } /* end if */ /* Free virtual selection */ if(source_dset->virtual_select) { if(H5S_close(source_dset->virtual_select) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release virtual selection") source_dset->virtual_select = NULL; } /* end if */ /* Free clipped source selection */ if(source_dset->clipped_source_select) { if(source_dset->clipped_source_select != virtual_ent->source_select) if(H5S_close(source_dset->clipped_source_select) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release clipped source selection") source_dset->clipped_source_select = NULL; } /* end if */ /* The projected memory space should never exist when this function is * called */ HDassert(!source_dset->projected_mem_space); /* Note the lack of a done: label. This is because there are no HGOTO_ERROR * calls. If one is added, a done: label must also be added */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_reset_source_dset() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_str_append * * Purpose: Appends src_len bytes of the string src to the position *p * in the buffer *buf (allocating *buf if necessary). * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * May 19, 2015 * *------------------------------------------------------------------------- */ static herr_t H5D__virtual_str_append(const char *src, size_t src_len, char **p, char **buf, size_t *buf_size) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(src); HDassert(src_len > 0); HDassert(p); HDassert(buf); HDassert(*p >= *buf); HDassert(buf_size); /* Allocate or extend buffer if necessary */ if(!*buf) { HDassert(!*p); HDassert(*buf_size == 0); /* Allocate buffer */ if(NULL == (*buf = (char *)H5MM_malloc(src_len + (size_t)1))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to allocate name segment struct") *buf_size = src_len + (size_t)1; *p = *buf; } /* end if */ else { size_t p_offset = (size_t)(*p - *buf); /* Offset of p within buf */ /* Extend buffer if necessary */ if((p_offset + src_len + (size_t)1) > *buf_size) { char *tmp_buf; size_t tmp_buf_size; /* Calculate new size of buffer */ tmp_buf_size = MAX(p_offset + src_len + (size_t)1, *buf_size * (size_t)2); /* Reallocate buffer */ if(NULL == (tmp_buf = (char *)H5MM_realloc(*buf, tmp_buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to reallocate name segment buffer") *buf = tmp_buf; *buf_size = tmp_buf_size; *p = *buf + p_offset; } /* end if */ } /* end else */ /* Copy string to *p. Note that since src in not NULL terminated, we must * use memcpy */ (void)HDmemcpy(*p, src, src_len); /* Advance *p */ *p += src_len; /* Add NULL terminator */ **p = '\0'; done: FUNC_LEAVE_NOAPI(ret_value); } /* end H5D__virtual_str_append() */ /*------------------------------------------------------------------------- * Function: H5D_virtual_parse_source_name * * Purpose: Parses a source file or dataset name. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * May 18, 2015 * *------------------------------------------------------------------------- */ herr_t H5D_virtual_parse_source_name(const char *source_name, H5O_storage_virtual_name_seg_t **parsed_name, size_t *static_strlen, size_t *nsubs) { H5O_storage_virtual_name_seg_t *tmp_parsed_name = NULL; H5O_storage_virtual_name_seg_t **tmp_parsed_name_p = &tmp_parsed_name; size_t tmp_static_strlen; size_t tmp_strlen; size_t tmp_nsubs = 0; const char *p; const char *pct; char *name_seg_p = NULL; size_t name_seg_size = 0; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) /* Sanity check */ HDassert(source_name); HDassert(parsed_name); HDassert(static_strlen); HDassert(nsubs); /* Initialize p and tmp_static_strlen */ p = source_name; tmp_static_strlen = tmp_strlen = HDstrlen(source_name); /* Iterate over name */ /* Note this will not work with UTF-8! We should support this eventually * -NAF 5/18/2015 */ while((pct = HDstrchr(p, '%'))) { HDassert(pct >= p); /* Allocate name segment struct if necessary */ if(!*tmp_parsed_name_p) if(NULL == (*tmp_parsed_name_p = H5FL_CALLOC(H5O_storage_virtual_name_seg_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to allocate name segment struct") /* Check for type of format specifier */ if(pct[1] == 'b') { /* Check for blank string before specifier */ if(pct != p) /* Append string to name segment */ if(H5D__virtual_str_append(p, (size_t)(pct - p), &name_seg_p, &(*tmp_parsed_name_p)->name_segment, &name_seg_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to append name segment") /* Update other variables */ tmp_parsed_name_p = &(*tmp_parsed_name_p)->next; tmp_static_strlen -= 2; tmp_nsubs++; name_seg_p = NULL; name_seg_size = 0; } /* end if */ else if(pct[1] == '%') { /* Append string to name segment (include first '%') */ if(H5D__virtual_str_append(p, (size_t)(pct - p) + (size_t)1, &name_seg_p, &(*tmp_parsed_name_p)->name_segment, &name_seg_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to append name segment") /* Update other variables */ tmp_static_strlen -= 1; } /* end else */ else HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid format specifier") p = pct + 2; } /* end while */ /* Copy last segment of name, if any, unless there were no substitutions */ if(tmp_nsubs > 0) { HDassert(p >= source_name); if(*p == '\0') HDassert((size_t)(p - source_name) == tmp_strlen); else { HDassert((size_t)(p - source_name) < tmp_strlen); /* Allocate name segment struct if necessary */ if(!*tmp_parsed_name_p) if(NULL == (*tmp_parsed_name_p = H5FL_CALLOC(H5O_storage_virtual_name_seg_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to allocate name segment struct") /* Append string to name segment */ if(H5D__virtual_str_append(p, tmp_strlen - (size_t)(p - source_name), &name_seg_p, &(*tmp_parsed_name_p)->name_segment, &name_seg_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to append name segment") } /* end else */ } /* end if */ /* Set return values */ *parsed_name = tmp_parsed_name; tmp_parsed_name = NULL; *static_strlen = tmp_static_strlen; *nsubs = tmp_nsubs; done: if(tmp_parsed_name) { HDassert(ret_value < 0); H5D_virtual_free_parsed_name(tmp_parsed_name); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_virtual_parse_source_name() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_copy_parsed_name * * Purpose: Deep copies a parsed source file or dataset name. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * May 19, 2015 * *------------------------------------------------------------------------- */ static herr_t H5D__virtual_copy_parsed_name(H5O_storage_virtual_name_seg_t **dst, H5O_storage_virtual_name_seg_t *src) { H5O_storage_virtual_name_seg_t *tmp_dst = NULL; H5O_storage_virtual_name_seg_t *p_src = src; H5O_storage_virtual_name_seg_t **p_dst = &tmp_dst; herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC /* Sanity check */ HDassert(dst); /* Walk over parsed name, duplicating it */ while(p_src) { /* Allocate name segment struct */ if(NULL == (*p_dst = H5FL_CALLOC(H5O_storage_virtual_name_seg_t))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to allocate name segment struct") /* Duplicate name segment */ if(p_src->name_segment) { if(NULL == ((*p_dst)->name_segment = HDstrdup(p_src->name_segment))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to duplicate name segment") } /* end if */ else (*p_dst)->name_segment = NULL; /* Advance pointers */ p_src = p_src->next; p_dst = &(*p_dst)->next; } /* end while */ /* Set dst */ *dst = tmp_dst; tmp_dst = NULL; done: if(tmp_dst) { HDassert(ret_value < 0); H5D_virtual_free_parsed_name(tmp_dst); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_copy_parsed_name() */ /*------------------------------------------------------------------------- * Function: H5D_virtual_free_parsed_name * * Purpose: Frees the provided parsed name. * * Return: void * * Programmer: Neil Fortner * May 19, 2015 * *------------------------------------------------------------------------- */ void H5D_virtual_free_parsed_name(H5O_storage_virtual_name_seg_t *name_seg) { H5O_storage_virtual_name_seg_t *next_seg; FUNC_ENTER_NOAPI_NOERR /* Walk name segments, freeing them */ while(name_seg) { (void)H5MM_xfree(name_seg->name_segment); next_seg = name_seg->next; (void)H5FL_FREE(H5O_storage_virtual_name_seg_t, name_seg); name_seg = next_seg; } /* end while */ FUNC_LEAVE_NOAPI_VOID } /* end H5D_virtual_free_parsed_name() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_build_source_name * * Purpose: Builds a source file or dataset name from a parsed name. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * May 18, 2015 * *------------------------------------------------------------------------- */ 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) { char *tmp_name = NULL; /* Name buffer */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(source_name); HDassert(built_name); /* Check for static name */ if(nsubs == 0) { HDassert(!parsed_name); *built_name = source_name; } /* end if */ else { const H5O_storage_virtual_name_seg_t *name_seg = parsed_name; char *p; hsize_t blockno_down = blockno; size_t blockno_len = 1; size_t name_len; size_t name_len_rem; size_t seg_len; size_t nsubs_rem = nsubs; HDassert(parsed_name); /* Calculate length of printed block number */ do { blockno_down /= (hsize_t)10; if(blockno_down == 0) break; blockno_len++; } while(1); /* Calculate length of name buffer */ name_len_rem = name_len = static_strlen + (nsubs * blockno_len) + (size_t)1; /* Allocate name buffer */ if(NULL == (tmp_name = (char *)H5MM_malloc(name_len))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to allocate name buffer") p = tmp_name; /* Build name */ do { /* Add name segment */ if(name_seg->name_segment) { seg_len = HDstrlen(name_seg->name_segment); HDassert(seg_len > 0); HDassert(seg_len < name_len_rem); HDstrncpy(p, name_seg->name_segment, name_len_rem); name_len_rem -= seg_len; p += seg_len; } /* end if */ /* Add block number */ if(nsubs_rem > 0) { HDassert(blockno_len < name_len_rem); if(HDsnprintf(p, name_len_rem, "%llu", (long long unsigned)blockno) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write block number to string") name_len_rem -= blockno_len; p += blockno_len; nsubs_rem--; } /* end if */ /* Advance name_seg */ name_seg = name_seg->next; } while(name_seg); /* Assign built_name */ *built_name = tmp_name; tmp_name = NULL; } /* end else */ done: if(tmp_name) { HDassert(ret_value < 0); H5MM_free(tmp_name); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_build_source_name() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_set_extent_unlim * * Purpose: Sets the extent of the virtual dataset by checking the * extents of source datasets where an unlimited selection * matching. Dimensions that are not unlimited in any * virtual mapping selections are not affected. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * April 22, 2015 * *------------------------------------------------------------------------- */ herr_t H5D__virtual_set_extent_unlim(const H5D_t *dset, hid_t dxpl_id) { H5O_storage_virtual_t *storage; hsize_t new_dims[H5S_MAX_RANK]; hsize_t curr_dims[H5S_MAX_RANK]; hsize_t clip_size; int rank; hbool_t changed = FALSE; /* Whether the VDS extent changed */ H5S_t *tmp_space = NULL; /* Temporary dataspace */ size_t i, j, k; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(dset); storage = &dset->shared->layout.storage.u.virt; HDassert(dset->shared->layout.storage.type == H5D_VIRTUAL); HDassert((storage->view == H5D_VDS_FIRST_MISSING) || (storage->view == H5D_VDS_LAST_AVAILABLE)); /* Get rank of VDS */ if((rank = H5S_GET_EXTENT_NDIMS(dset->shared->space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get number of dimensions") /* Initialize new_dims to HSIZE_UNDEF */ for(i = 0; i < (size_t)rank; i++) new_dims[i] = HSIZE_UNDEF; /* Iterate over mappings */ for(i = 0; i < storage->list_nalloc; i++) /* Check for unlimited dimension */ if(storage->list[i].unlim_dim_virtual >= 0) { /* Check for "printf" source dataset resolution */ if(storage->list[i].unlim_dim_source >= 0 ) { /* 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) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open source dataset") /* Check if source dataset is open */ if(storage->list[i].source_dset.dset) { /* Retrieve current source dataset extent and patch mapping */ if(H5S_extent_copy(storage->list[i].source_select, storage->list[i].source_dset.dset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy source dataspace extent") /* Get source space dimenstions */ if(H5S_get_simple_extent_dims(storage->list[i].source_select, curr_dims, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get source space dimensions") /* Check if the source extent in the unlimited dimension * changed since the last time the VDS extent/mapping * was updated */ if(curr_dims[storage->list[i].unlim_dim_source] == storage->list[i].unlim_extent_source) /* Use cached result for clip size */ clip_size = storage->list[i].clip_size_virtual; else { /* Copy source mapping */ if(NULL == (tmp_space = H5S_copy(storage->list[i].source_select, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy source selection") /* Clip temporary source space to source extent */ if(H5S_hyper_clip_unlim(tmp_space, curr_dims[storage->list[i].unlim_dim_source])) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "failed to clip unlimited selection") /* Get size that virtual selection would be clipped to * to match size of source selection */ if(H5S_hyper_get_clip_extent(storage->list[i].source_dset.virtual_select, tmp_space, &clip_size, storage->view == H5D_VDS_FIRST_MISSING) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get hyperslab clip size") /* Close tmp_space */ if(H5S_close(tmp_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release dataspace") tmp_space = NULL; /* If we are setting the extent by the last available * data, clip virtual_select and source_select. Note * that if we used the cached clip_size above or it * happens to be the same, the virtual selection will * already be clipped to the correct size. Likewise, * if we used the cached clip_size the source selection * will already be correct. */ if(storage->view == H5D_VDS_LAST_AVAILABLE) { if(clip_size != storage->list[i].clip_size_virtual) { /* Close previous clipped virtual selection, if * any */ if(storage->list[i].source_dset.clipped_virtual_select) { HDassert(storage->list[i].source_dset.clipped_virtual_select != storage->list[i].source_dset.virtual_select); if(H5S_close(storage->list[i].source_dset.clipped_virtual_select) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release clipped virtual dataspace") } /* end if */ /* Copy virtual selection */ if(NULL == (storage->list[i].source_dset.clipped_virtual_select = H5S_copy(storage->list[i].source_dset.virtual_select, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy virtual selection") /* Clip virtual selection */ if(H5S_hyper_clip_unlim(storage->list[i].source_dset.clipped_virtual_select, clip_size)) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "failed to clip unlimited selection") } /* end if */ /* Close previous clipped source selection, if any */ if(storage->list[i].source_dset.clipped_source_select) { HDassert(storage->list[i].source_dset.clipped_source_select != storage->list[i].source_select); if(H5S_close(storage->list[i].source_dset.clipped_source_select) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release clipped source dataspace") } /* end if */ /* Copy source selection */ if(NULL == (storage->list[i].source_dset.clipped_source_select = H5S_copy(storage->list[i].source_select, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy source selection") /* Clip source selection */ if(H5S_hyper_clip_unlim(storage->list[i].source_dset.clipped_source_select, curr_dims[storage->list[i].unlim_dim_source])) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "failed to clip unlimited selection") } /* end if */ /* 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; } /* end else */ } /* end if */ else clip_size = 0; } /* end if */ else { /* printf mapping */ hsize_t first_missing = 0; /* First missing dataset in the current block of missing datasets */ /* Search for source datasets */ HDassert(storage->printf_gap != HSIZE_UNDEF); for(j = 0; j <= (storage->printf_gap + first_missing); j++) { /* Check for running out of space in sub_dset array */ if(j >= (hsize_t)storage->list[i].sub_dset_nalloc) { if(storage->list[i].sub_dset_nalloc == 0) { /* Allocate sub_dset */ if(NULL == (storage->list[i].sub_dset = (H5O_storage_virtual_srcdset_t *)H5MM_calloc(H5D_VIRTUAL_DEF_SUB_DSET_SIZE * sizeof(H5O_storage_virtual_srcdset_t)))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to allocate sub dataset array") storage->list[i].sub_dset_nalloc = H5D_VIRTUAL_DEF_SUB_DSET_SIZE; } /* end if */ else { H5O_storage_virtual_srcdset_t *tmp_sub_dset; HDassert(0 && "Checking code coverage..."); //VDSINC /* Extend sub_dset */ if(NULL == (tmp_sub_dset = (H5O_storage_virtual_srcdset_t *)H5MM_realloc(storage->list[i].sub_dset, 2 * storage->list[i].sub_dset_nalloc * sizeof(H5O_storage_virtual_srcdset_t)))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "unable to extend sub dataset array") /* Clear new space in sub_dset */ (void)HDmemset(&storage->list[i].sub_dset[storage->list[i].sub_dset_nalloc], 0, storage->list[i].sub_dset_nalloc * sizeof(H5O_storage_virtual_srcdset_t)); /* Update sub_dset_nalloc */ storage->list[i].sub_dset_nalloc *= 2; } /* end else */ } /* end if */ /* Check if the dataset is already open */ if(storage->list[i].sub_dset[j].dset) first_missing = j + 1; else { /* Resolve file name */ if(!storage->list[i].sub_dset[j].file_name) if(H5D__virtual_build_source_name(storage->list[i].source_dset.file_name, storage->list[i].parsed_source_file_name, storage->list[i].psfn_static_strlen, storage->list[i].psfn_nsubs, j, &storage->list[i].sub_dset[j].file_name) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to build source file name") /* Resolve dset name */ if(!storage->list[i].sub_dset[j].dset_name) if(H5D__virtual_build_source_name(storage->list[i].source_dset.dset_name, storage->list[i].parsed_source_dset_name, storage->list[i].psdn_static_strlen, storage->list[i].psdn_nsubs, j, &storage->list[i].sub_dset[j].dset_name) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to build source dataset name") /* Resolve virtual selection for block */ if(!storage->list[i].sub_dset[j].virtual_select) if(NULL == (storage->list[i].sub_dset[j].virtual_select = H5S_hyper_get_unlim_block(storage->list[i].source_dset.virtual_select, j))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get block in unlimited selection") /* Initialize clipped selections */ if(!storage->list[i].sub_dset[j].clipped_source_select) storage->list[i].sub_dset[j].clipped_source_select = storage->list[i].source_select; if(!storage->list[i].sub_dset[j].clipped_virtual_select) 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) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open source dataset") /* Update first_missing */ if(storage->list[i].sub_dset[j].dset) first_missing = j + 1; } /* end else */ } /* end for */ /* Check if the size changed */ if((first_missing == (hsize_t)storage->list[i].sub_dset_nused) && (storage->list[i].clip_size_virtual != HSIZE_UNDEF)) /* Use cached clip_size */ clip_size = storage->list[i].clip_size_virtual; else { /* Check for no datasets */ if(first_missing == 0) /* Set clip size to 0 */ clip_size = (hsize_t)0; else { hsize_t bounds_start[H5S_MAX_RANK]; hsize_t bounds_end[H5S_MAX_RANK]; /* Get clip size from selection */ if(storage->view == H5D_VDS_LAST_AVAILABLE) { /* Get bounds from last valid virtual selection */ if(H5S_SELECT_BOUNDS(storage->list[i].sub_dset[first_missing - (hsize_t)1].virtual_select, bounds_start, bounds_end) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get selection bounds") /* Set clip_size to bounds_end in unlimited * dimension */ clip_size = bounds_end[storage->list[i].unlim_dim_virtual] + (hsize_t)1; } /* end if */ else { /* Get bounds from first missing virtual selection */ if(H5S_SELECT_BOUNDS(storage->list[i].sub_dset[first_missing].virtual_select, bounds_start, bounds_end) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get selection bounds") /* Set clip_size to bounds_start in unlimited * dimension */ clip_size = bounds_start[storage->list[i].unlim_dim_virtual]; } /* end else */ } /* end else */ /* Set sub_dset_nused and clip_size_virtual */ storage->list[i].sub_dset_nused = (size_t)first_missing; storage->list[i].clip_size_virtual = clip_size; } /* end else */ } /* end else */ /* Update new_dims */ if((new_dims[storage->list[i].unlim_dim_virtual] == HSIZE_UNDEF) || (storage->view == H5D_VDS_FIRST_MISSING ? (clip_size < (hsize_t)new_dims[storage->list[i].unlim_dim_virtual]) : (clip_size > (hsize_t)new_dims[storage->list[i].unlim_dim_virtual]))) new_dims[storage->list[i].unlim_dim_virtual] = clip_size; } /* end if */ /* Get current VDS dimensions */ if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get VDS dimensions") /* Calculate new extent */ for(i = 0; i < (size_t)rank; i++) { if(new_dims[i] == HSIZE_UNDEF) new_dims[i] = curr_dims[i]; else if(new_dims[i] < storage->min_dims[i]) { HDassert(0 && "Checking code coverage..."); //VDSINC new_dims[i] = storage->min_dims[i]; } //VDSINC if(new_dims[i] != curr_dims[i]) changed = TRUE; } /* end for */ /* If we did not change the VDS dimensions, there is nothing more to update */ if(changed || (!storage->init && (storage->view == H5D_VDS_FIRST_MISSING))) { /* 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") /* Iterate over mappings again to update source selections and virtual * mapping extents */ for(i = 0; i < storage->list_nalloc; i++) { /* If there is an unlimited dimension, we are setting extent by the * minimum of mappings, and the virtual extent in the unlimited * dimension has changed since the last time the VDS extent/mapping * was updated, we must adjust the selections */ if((storage->list[i].unlim_dim_virtual >= 0) && (storage->view == H5D_VDS_FIRST_MISSING) && (new_dims[storage->list[i].unlim_dim_virtual] != storage->list[i].unlim_extent_virtual)) { /* Check for "printf" style mapping */ if(storage->list[i].unlim_dim_source >= 0) { /* Non-printf mapping */ /* Close previous clipped virtual selection, if any */ if(storage->list[i].source_dset.clipped_virtual_select) { HDassert(storage->list[i].source_dset.clipped_virtual_select != storage->list[i].source_dset.virtual_select); if(H5S_close(storage->list[i].source_dset.clipped_virtual_select) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release clipped virtual dataspace") } /* end if */ /* Copy virtual selection */ if(NULL == (storage->list[i].source_dset.clipped_virtual_select = H5S_copy(storage->list[i].source_dset.virtual_select, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy virtual selection") /* Clip space to virtual extent */ if(H5S_hyper_clip_unlim(storage->list[i].source_dset.clipped_virtual_select, new_dims[storage->list[i].unlim_dim_source])) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "failed to clip unlimited selection") /* Get size that source selection will be clipped to to * match size of source selection */ if(H5S_hyper_get_clip_extent(storage->list[i].source_select, storage->list[i].source_dset.clipped_virtual_select, &clip_size, FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get hyperslab clip size") /* Check if the clip size changed */ if(clip_size != storage->list[i].clip_size_source) { /* Close previous clipped source selection, if any */ if(storage->list[i].source_dset.clipped_source_select) { HDassert(storage->list[i].source_dset.clipped_source_select != storage->list[i].source_select); if(H5S_close(storage->list[i].source_dset.clipped_source_select) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release clipped source dataspace") } /* end if */ /* Copy source selection */ if(NULL == (storage->list[i].source_dset.clipped_source_select = H5S_copy(storage->list[i].source_select, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy source selection") /* Clip source selection */ if(H5S_hyper_clip_unlim(storage->list[i].source_dset.clipped_source_select, clip_size)) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "failed to clip unlimited selection") /* Update cached value clip_size_source */ storage->list[i].clip_size_source = clip_size; } /* end if */ } /* end if */ else { /* printf mapping */ hsize_t first_inc_block; hbool_t partial_block; /* Get index of first incomplete block in virtual * selection */ first_inc_block = H5S_hyper_get_first_inc_block(storage->list[i].source_dset.virtual_select, new_dims[storage->list[i].unlim_dim_virtual], &partial_block); /* Iterate over sub datasets */ for(j = 0; j < storage->list[i].sub_dset_nalloc; j++) { /* Close previous clipped source selection, if any */ if(storage->list[i].sub_dset[j].clipped_source_select != storage->list[i].source_select) { if(storage->list[i].sub_dset[j].clipped_source_select) if(H5S_close(storage->list[i].sub_dset[j].clipped_source_select) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release clipped source dataspace") storage->list[i].sub_dset[j].clipped_source_select = storage->list[i].source_select; } /* end if */ /* Close previous clipped virtual selection, if any */ if(storage->list[i].sub_dset[j].clipped_virtual_select != storage->list[i].sub_dset[j].virtual_select) { if(storage->list[i].sub_dset[j].clipped_virtual_select) if(H5S_close(storage->list[i].sub_dset[j].clipped_virtual_select) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "unable to release clipped virtual dataspace") storage->list[i].sub_dset[j].clipped_virtual_select = storage->list[i].sub_dset[j].virtual_select; } /* end if */ /* Check for partial block */ else if(partial_block && (j == (size_t)first_inc_block)) { /* Partial block, must clip source and virtual * selections */ hsize_t start[H5S_MAX_RANK]; /* Get bounds of virtual selection */ if(H5S_SELECT_BOUNDS(storage->list[i].sub_dset[j].virtual_select, start, curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get selection bounds") /* Convert bounds to extent (add 1) */ for(k = 0; k < (size_t)rank; k++) curr_dims[k]++; /* Temporarily set extent of virtual selection to bounds */ if(H5S_set_extent(storage->list[i].sub_dset[j].virtual_select, curr_dims) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to modify size of data space") /* Copy virtual selection */ if(NULL == (storage->list[i].sub_dset[j].clipped_virtual_select = H5S_copy(storage->list[i].sub_dset[j].virtual_select, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy virtual selection") /* Clip virtual selection to real virtual extent */ (void)HDmemset(start, 0, sizeof(start)); if(H5S_select_hyperslab(storage->list[i].sub_dset[j].clipped_virtual_select, H5S_SELECT_AND, start, NULL, new_dims, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to clip hyperslab") /* Project intersection of virtual space and clipped * virtual space onto source space */ 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) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto memory space") } /* end if */ else if(j >= (size_t)first_inc_block) { /* Unused block, clear clipped source and virtual * selections */ storage->list[i].sub_dset[j].clipped_source_select = NULL; storage->list[i].sub_dset[j].clipped_virtual_select = NULL; } /* end if */ } /* end for */ } /* end else */ /* Update cached value unlim_extent_virtual */ storage->list[i].unlim_extent_virtual = new_dims[storage->list[i].unlim_dim_virtual]; } /* end if */ /* 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") 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") /* 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") 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") } /* end if */ else HDassert(!storage->list[i].sub_dset[j].clipped_virtual_select); } /* end for */ } /* end if */ /* Call H5D__mark so dataspace is updated on disk? VDSINC */ /* Mark layout as fully initialized */ storage->init = TRUE; done: /* Close temporary space */ if(tmp_space) { HDassert(ret_value < 0); if(H5S_close(tmp_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close temporary space") } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_set_extent_unlim() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_init * * Purpose: Initialize the virtual layout information for a dataset. * This is called when the dataset is initialized. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * Thursday, April 30, 2015 * *------------------------------------------------------------------------- */ herr_t H5D__virtual_init(H5F_t H5_ATTR_UNUSED *f, hid_t H5_ATTR_UNUSED dxpl_id, 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 */ size_t i; /* Local index variables */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(dset); storage = &dset->shared->layout.storage.u.virt; HDassert(storage->list || (storage->list_nused == 0)); /* Patch the virtual selection dataspaces */ for(i = 0; i < storage->list_nused; i++) { if(storage->list[i].virtual_space_status != H5O_VIRTUAL_STATUS_CORRECT) { if(H5S_extent_copy(storage->list[i].source_dset.virtual_select, dset->shared->space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't copy virtual dataspace extent") storage->list[i].virtual_space_status = H5O_VIRTUAL_STATUS_CORRECT; HDassert(storage->list[i].sub_dset_nalloc == 0); } /* end if */ } /* end for */ /* Get dataset access property list */ if(NULL == (dapl = (H5P_genplist_t *)H5I_object(dapl_id))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for dapl ID") /* Get view option */ if(H5P_get(dapl, H5D_ACS_VDS_VIEW_NAME, &storage->view) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get virtual view option") /* Get printf gap if view is H5D_VDS_LAST_AVAILABLE, otherwise set to 0 */ if(storage->view == H5D_VDS_LAST_AVAILABLE) { if(H5P_get(dapl, H5D_ACS_VDS_PRINTF_GAP_NAME, &storage->printf_gap) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get virtual printf gap") } /* end if */ else storage->printf_gap = (hsize_t)0; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_init() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_is_space_alloc * * Purpose: Query if space is allocated for layout * * Return: TRUE if space is allocated * FALSE if it is not * Negative on failure * * Programmer: Neil Fortner * February 6, 2015 * *------------------------------------------------------------------------- */ hbool_t H5D__virtual_is_space_alloc(const H5O_storage_t H5_ATTR_UNUSED *storage) { hbool_t ret_value; /* Return value */ FUNC_ENTER_PACKAGE_NOERR /* Need to decide what to do here. For now just return TRUE VDSINC */ ret_value = TRUE;//storage->u.virt.serial_list_hobjid.addr != HADDR_UNDEF; FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_is_space_alloc() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_pre_io * * Purpose: Project all virtual mappings onto mem_space, with the * results stored in projected_mem_space for each mapping. * Opens all source datasets if possible. The total number * of elements is stored in tot_nelmts. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * June 3, 2015 * *------------------------------------------------------------------------- */ 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) { 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; hbool_t bounds_init = FALSE; /* Whether bounds_start, bounds_end, and rank are valid */ size_t i, j; /* Local index variables */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(storage); HDassert(mem_space); HDassert(file_space); HDassert(tot_nelmts); /* Initialize layout if necessary */ if(!storage->init) {} //VDSINC /* Initialize tot_nelmts */ *tot_nelmts = 0; /* Iterate over mappings */ for(i = 0; i < storage->list_nused; i++) { /* Sanity check that the virtual space has been patched by now */ HDassert(storage->list[i].virtual_space_status == H5O_VIRTUAL_STATUS_CORRECT); /* Check for "printf" source dataset resolution */ if(storage->list[i].parsed_source_file_name || storage->list[i].parsed_source_dset_name) { hbool_t partial_block; HDassert(storage->list[i].unlim_dim_virtual >= 0); /* Get selection bounds if necessary */ if(!bounds_init) { /* Get rank of VDS */ if((rank = H5S_GET_EXTENT_NDIMS(io_info->dset->shared->space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get number of dimensions") /* Get selection bounds */ if(H5S_SELECT_BOUNDS(file_space, bounds_start, bounds_end) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get selection bounds") /* Adjust bounds_end to represent the extent just enclosing them * (add 1) */ for(j = 0; j < (size_t)rank; j++) bounds_end[j]++; /* Bounds are now initialized */ bounds_init = TRUE; } /* end if */ /* Get index of first block in virtual selection */ storage->list[i].sub_dset_io_start = (size_t)H5S_hyper_get_first_inc_block(storage->list[i].source_dset.virtual_select, bounds_start[storage->list[i].unlim_dim_virtual], NULL); /* Get index of first block outside of virtual selection */ storage->list[i].sub_dset_io_end = (size_t)H5S_hyper_get_first_inc_block(storage->list[i].source_dset.virtual_select, bounds_end[storage->list[i].unlim_dim_virtual], &partial_block); if(partial_block) storage->list[i].sub_dset_io_end++; if(storage->list[i].sub_dset_io_end > storage->list[i].sub_dset_nused) storage->list[i].sub_dset_io_end = storage->list[i].sub_dset_nused; /* Iterate over sub-source dsets */ for(j = storage->list[i].sub_dset_io_start; j < storage->list[i].sub_dset_io_end; j++) { /* There should always be a clipped virtual selection here */ HDassert(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) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto memory space") /* Check number of elements selected */ if((select_nelmts = (hssize_t)H5S_GET_SELECT_NPOINTS(storage->list[i].sub_dset[j].projected_mem_space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get number of elements in selection") /* Check if anything is selected */ if(select_nelmts > (hssize_t)0) { /* 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->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open source dataset") /* If the source dataset is not open, mark the selected * elements as zero so projected_mem_space is freed */ if(!storage->list[i].sub_dset[j].dset) select_nelmts = (hssize_t)0; } /* end if */ /* If there are not elements selected in this mapping, free * projected_mem_space, otherwise update tot_nelmts */ if(select_nelmts == (hssize_t)0) { if(H5S_close(storage->list[i].sub_dset[j].projected_mem_space) < 0) 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 *tot_nelmts += (hsize_t)select_nelmts; } /* end for */ } /* end if */ else { HDassert(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) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto memory space") /* Check number of elements selected, add to tot_nelmts */ if((select_nelmts = (hssize_t)H5S_GET_SELECT_NPOINTS(storage->list[i].source_dset.projected_mem_space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get number of elements in selection") /* Check if anything is selected */ if(select_nelmts > (hssize_t)0) { /* 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], &storage->list[i].source_dset, io_info->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open source dataset") /* If the source dataset is not open, mark the selected elements * as zero so projected_mem_space is freed */ if(!storage->list[i].source_dset.dset) { HDassert(0 && "Checking code coverage..."); //VDSINC select_nelmts = (hssize_t)0; } //VDSINC } /* end if */ /* If there are not elements selected in this mapping, free * projected_mem_space, otherwise update tot_nelmts */ if(select_nelmts == (hssize_t)0) { if(H5S_close(storage->list[i].source_dset.projected_mem_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close projected memory space") storage->list[i].source_dset.projected_mem_space = NULL; } /* end if */ else *tot_nelmts += (hsize_t)select_nelmts; } /* end else */ } /* end for */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_pre_io() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_post_io * * Purpose: VDSINC * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * June 4, 2015 * *------------------------------------------------------------------------- */ static herr_t H5D__virtual_post_io(H5O_storage_virtual_t *storage) { size_t i, j; /* Local index variables */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(storage); /* Iterate over mappings */ for(i = 0; i < storage->list_nused; i++) /* Check for "printf" source dataset resolution */ if(storage->list[i].parsed_source_file_name || storage->list[i].parsed_source_dset_name) { /* Iterate over sub-source dsets */ for(j = storage->list[i].sub_dset_io_start; j < storage->list[i].sub_dset_io_end; j++) /* Close projected memory space */ if(storage->list[i].sub_dset[j].projected_mem_space) { if(H5S_close(storage->list[i].sub_dset[j].projected_mem_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close temporary space") storage->list[i].sub_dset[j].projected_mem_space = NULL; } /* end if */ } /* end if */ else /* Close projected memory space */ if(storage->list[i].source_dset.projected_mem_space) { if(H5S_close(storage->list[i].source_dset.projected_mem_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close temporary space") storage->list[i].source_dset.projected_mem_space = NULL; } /* end if */ /* Note the lack of a done: label. This is because there are no HGOTO_ERROR * calls. If one is added, a done: label must also be added */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_post_io() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_read_one * * Purpose: Read from a singe source dataset in a virtual dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * May 15, 2015 * *------------------------------------------------------------------------- */ static herr_t H5D__virtual_read_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, const H5S_t *file_space, 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 */ FUNC_ENTER_STATIC HDassert(source_dset); /* Only perform I/O if there is a projected memory space, otherwise there * were no elements in the projection or the source dataset could not be * opened */ if(source_dset->projected_mem_space) { HDassert(source_dset->dset); HDassert(source_dset->clipped_source_select); /* 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) 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->dxpl_id, io_info->u.rbuf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read source dataset") /* Close projected_src_space */ if(H5S_close(projected_src_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close projected source space") projected_src_space = NULL; } /* end if */ done: /* Release allocated resources on failure */ if(projected_src_space) { HDassert(ret_value < 0); if(H5S_close(projected_src_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close projected source space") } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_read_one() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_read * * Purpose: Read from a virtual dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * February 6, 2015 * *------------------------------------------------------------------------- */ 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 H5_ATTR_UNUSED *fm) { 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 i, j; /* Local index variables */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(io_info); HDassert(io_info->u.rbuf); HDassert(type_info); HDassert(mem_space); HDassert(file_space); storage = &io_info->dset->shared->layout.storage.u.virt; HDassert((storage->view == H5D_VDS_FIRST_MISSING) || (storage->view == H5D_VDS_LAST_AVAILABLE)); /* Prepare for I/O operation */ if(H5D__virtual_pre_io(io_info, storage, file_space, mem_space, &tot_nelmts) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to prepare for I/O operation") /* Iterate over mappings */ for(i = 0; i < storage->list_nused; i++) { /* Sanity check that the virtual space has been patched by now */ HDassert(storage->list[i].virtual_space_status == H5O_VIRTUAL_STATUS_CORRECT); /* Check for "printf" source dataset resolution */ if(storage->list[i].parsed_source_file_name || storage->list[i].parsed_source_dset_name) { /* 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) 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) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read source dataset") } /* end for */ /* Fill unmapped part of buffer with fill value */ if(tot_nelmts != nelmts) { HDassert(tot_nelmts < nelmts); /* Start with fill space equal to memory space */ if(NULL == (fill_space = H5S_copy(mem_space, FALSE, TRUE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy memory selection") /* Iterate over mappings */ for(i = 0; i < storage->list_nused; i++) /* Check for "printf" source dataset resolution */ if(storage->list[i].parsed_source_file_name || storage->list[i].parsed_source_dset_name) { /* Iterate over sub-source dsets */ for(j = storage->list[i].sub_dset_io_start; j < storage->list[i].sub_dset_io_end; j++) if(storage->list[i].sub_dset[j].projected_mem_space) if(H5S_select_subtract(fill_space, storage->list[i].sub_dset[j].projected_mem_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "unable to clip fill selection") } /* end if */ else if(storage->list[i].source_dset.projected_mem_space) /* Subtract projected memory space from fill space */ if(H5S_select_subtract(fill_space, storage->list[i].source_dset.projected_mem_space) < 0) 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->dxpl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "filling buf failed") #ifndef NDEBUG /* Make sure the total number of elements written (including fill * values) == nelmts */ { hssize_t select_nelmts; /* Number of elements in selection */ /* Get number of elements in fill dataspace */ if((select_nelmts = (hssize_t)H5S_GET_SELECT_NPOINTS(fill_space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get number of elements in selection") /* Verify number of elements is correct */ HDassert((tot_nelmts + (hsize_t)select_nelmts) == nelmts); } /* end block */ #endif /* NDEBUG */ } /* end if */ done: /* Cleanup I/O operation */ if(H5D__virtual_post_io(storage) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't cleanup I/O operation") /* Close fill space */ if(fill_space) if(H5S_close(fill_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close fill space") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_read() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_write_one * * Purpose: Write to a singe source dataset in a virtual dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * May 15, 2015 * *------------------------------------------------------------------------- */ static herr_t H5D__virtual_write_one(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, const H5S_t *file_space, 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 */ FUNC_ENTER_STATIC HDassert(source_dset); /* Only perform I/O if there is a projected memory space, otherwise there * were no elements in the projection */ if(source_dset->projected_mem_space) { HDassert(source_dset->dset); HDassert(source_dset->clipped_source_select); /* Extend source dataset if necessary and there is an unlimited * dimension VDSINC */ /* 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) 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->dxpl_id, io_info->u.wbuf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write to source dataset") /* Close projected_src_space */ if(H5S_close(projected_src_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close projected source space") projected_src_space = NULL; } /* end if */ done: /* Release allocated resources on failure */ if(projected_src_space) { HDassert(ret_value < 0); if(H5S_close(projected_src_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close projected source space") } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_write_one() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_write * * Purpose: Write to a virtual dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * February 6, 2015 * *------------------------------------------------------------------------- */ 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 H5_ATTR_UNUSED *fm) { H5O_storage_virtual_t *storage; /* Convenient pointer into layout struct */ hsize_t tot_nelmts; /* Total number of elements mapped to mem_space */ size_t i, j; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(io_info); HDassert(io_info->u.wbuf); HDassert(type_info); HDassert(mem_space); HDassert(file_space); storage = &io_info->dset->shared->layout.storage.u.virt; HDassert((storage->view == H5D_VDS_FIRST_MISSING) || (storage->view == H5D_VDS_LAST_AVAILABLE)); /* Prepare for I/O operation */ if(H5D__virtual_pre_io(io_info, storage, file_space, 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 * written */ if(tot_nelmts != nelmts) { HDassert(0 && "Checking code coverage..."); //VDSINC HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "write requested to unmapped portion of virtual dataset") } //VDSINC /* Iterate over mappings */ for(i = 0; i < storage->list_nused; i++) { /* Sanity check that virtual space has been patched by now */ HDassert(storage->list[i].virtual_space_status == H5O_VIRTUAL_STATUS_CORRECT); /* Check for "printf" source dataset resolution */ if(storage->list[i].parsed_source_file_name || storage->list[i].parsed_source_dset_name) { /* Iterate over sub-source dsets */ for(j = storage->list[i].sub_dset_io_start; j < storage->list[i].sub_dset_io_end; j++) { HDassert(0 && "Checking code coverage..."); //VDSINC if(H5D__virtual_write_one(io_info, type_info, file_space, &storage->list[i].sub_dset[j]) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to write to source dataset") } //VDSINC } /* end if */ else /* Write to source dataset */ if(H5D__virtual_write_one(io_info, type_info, file_space, &storage->list[i].source_dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to write to source dataset") } /* end for */ done: /* Cleanup I/O operation */ if(H5D__virtual_post_io(storage) < 0) HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't cleanup I/O operation") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__virtual_write() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_flush * * Purpose: Writes all dirty data to disk. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * February 6, 2015 * *------------------------------------------------------------------------- */ static herr_t H5D__virtual_flush(H5D_t H5_ATTR_UNUSED *dset, hid_t H5_ATTR_UNUSED dxpl_id) { FUNC_ENTER_STATIC_NOERR /* Flush only open datasets */ /* No-op for now VDSINC */ FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D__virtual_flush() */ /*------------------------------------------------------------------------- * Function: H5D__virtual_copy * * Purpose: Copy virtual storage raw data from SRC file to DST file. * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * February 6, 2015 * *------------------------------------------------------------------------- */ herr_t H5D__virtual_copy(H5F_t H5_ATTR_UNUSED *f_src, const H5O_storage_virtual_t H5_ATTR_UNUSED *storage_src, H5F_t H5_ATTR_UNUSED *f_dst, H5O_storage_virtual_t H5_ATTR_UNUSED *storage_dst, H5T_t H5_ATTR_UNUSED *dt_src, H5O_copy_t H5_ATTR_UNUSED *cpy_info, hid_t H5_ATTR_UNUSED dxpl_id) { FUNC_ENTER_PACKAGE_NOERR HDassert(0 && "Not yet implemented...");//VDSINC FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D__virtual_copy() */