diff options
Diffstat (limited to 'tools/h5repack/h5repack_copy.c')
-rw-r--r-- | tools/h5repack/h5repack_copy.c | 108 |
1 files changed, 62 insertions, 46 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index 02a3c00..cdee6eb 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -80,8 +80,8 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t * -1 no *------------------------------------------------------------------------- */ - -int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) +int +copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) { int ret_value = 0; hid_t fidin = -1; @@ -126,6 +126,14 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed to close property list"); } + /* Create file access property list */ + if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list"); + + if(options->latest) + if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_libver_bounds failed to set format version bounds"); + /* Check if we need to create a non-default file creation property list */ if (options->latest || ub_size > 0) { /* Create file creation property list */ @@ -141,8 +149,7 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) /* Adjust group creation parameters for root group */ /* (So that it is created in "dense storage" form) */ - if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, - (unsigned) options->grp_indexed) < 0) + if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed to adjust group creation parameters for root group"); for (i = 0; i < 5; i++) { @@ -187,12 +194,6 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_index failed to configure the specified shared object header message index"); } /* if (nindex>0) */ - /* Create file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list"); - - if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_libver_bounds failed to set property for using latest version of the format"); } /* end if */ } /* end if */ #if defined (H5REPACK_DEBUG_USER_BLOCK) @@ -333,7 +334,7 @@ done: trav_table_free(travt); return ret_value; -} +} /* end copy_objects() */ /*------------------------------------------------------------------------- * Function: Get_hyperslab @@ -489,7 +490,7 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], done: return ret_value; -} +} /* end Get_hyperslab() */ /*------------------------------------------------------------------------- * Function: do_copy_objects @@ -545,7 +546,8 @@ done: *------------------------------------------------------------------------- */ -int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, +int +do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *options) /* repack options */ { int ret_value = 0; @@ -580,7 +582,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, unsigned crt_order_flags; /* group creation order flag */ unsigned i; unsigned u; - unsigned uf; + int ifil; int is_ref = 0; htri_t is_named; hbool_t limit_maxdims; @@ -686,8 +688,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, if (options->op_tbl->objs) { for (u = 0; u < options->op_tbl->nelems; u++) { if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) - for (uf = 0; uf < options->op_tbl->objs[uf].nfilters; uf++) { - if (options->op_tbl->objs[u].filter[uf].filtn > 0) + for (ifil = 0; ifil < options->op_tbl->objs[ifil].nfilters; ifil++) { + if (options->op_tbl->objs[u].filter[ifil].filtn > 0) req_filter = 1; } } @@ -745,8 +747,6 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed"); if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed"); - if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) - HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed"); if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed"); HDmemset(dims, 0, sizeof dims); @@ -755,6 +755,19 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, if (H5Dget_space_status(dset_in, &space_status) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed"); + /* If the input dataset has external storage, it must be contiguous. + * Accordingly, there would be no filter or chunk properties to preserve, + * so create a new DCPL. + * Otherwise, copy dcpl_in. + */ + if (H5Pget_external_count(dcpl_in)) { + if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed"); + } + else if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) { + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed"); + } + nelmts = 1; for (j = 0; j < rank; j++) nelmts *= dims[j]; @@ -765,7 +778,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT); else wtype_id = H5Tcopy(ftype_id); - } /* end if */ + } if ((msize = H5Tget_size(wtype_id)) == 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed"); @@ -809,7 +822,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, /* only if layout change requested for entire file or * individual obj */ - if (options->all_layout > 0 || req_obj_layout == 1) + if (options->all_layout > 0 || req_obj_layout == 1) { /*------------------------------------------------- * Unset the unlimited max dims if convert to other * than chunk layouts, because unlimited max dims @@ -836,7 +849,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, /* unset unlimited max dims */ if (limit_maxdims) H5Sset_extent_simple(f_space_id, rank, dims, NULL); - } + } /* end if not chunked */ + } /* end if layout change requested for entire file or individual object */ /*------------------------------------------------------------------------- * create the output dataset; @@ -853,7 +867,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed"); apply_f = 0; - } + } /* end if retry dataset create */ /*------------------------------------------------------------------------- * read/write @@ -914,7 +928,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, dset_layout = H5Pget_layout(dcpl_out); if (dset_layout == H5D_CHUNKED) dcpl_tmp = dcpl_out; /* writing dataset */ - else { /* if reading dataset is chunked */ + else { dset_layout = H5Pget_layout(dcpl_in); if (dset_layout == H5D_CHUNKED) dcpl_tmp = dcpl_in; /* reading dataset */ @@ -925,6 +939,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed"); hslab_buf = HDmalloc((size_t)hslab_nbytes); + if (hslab_buf == NULL) + HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "can't allocate space for hyperslab"); hslab_nelmts = hslab_nbytes / p_type_nbytes; hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL); @@ -951,12 +967,12 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed"); - } + } /* end if rank > 0 */ else { H5Sselect_all(f_space_id); H5Sselect_all(hslab_space); hs_select_nelmts = 1; - } /* rank */ + } /* end (else) rank == 0 */ if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed"); @@ -975,8 +991,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, hs_sel_offset[k - 1] = 0; else carry = 0; - } /* k */ - } /* elmtno */ + } + } /* end for (hyperslab selection loop) */ H5Sclose(hslab_space); /* free */ @@ -984,11 +1000,11 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, HDfree(hslab_buf); hslab_buf = NULL; } - } /* hyperslab read */ - } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */ + } /* end if reading/writing by hyperslab */ + } /* end if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) */ /*------------------------------------------------------------------------- - * amount of compression used + * print amount of compression used *------------------------------------------------------------------------- */ if (options->verbose) { @@ -1008,14 +1024,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0); /* print a message that the filter was not applied - (in case there was a filter) + * (in case there was a filter) */ if (has_filter && apply_s == 0) HDprintf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp); if (has_filter && apply_f == 0) HDprintf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name); - } /* verbose */ + } /* end if verbose (print compression) */ /*------------------------------------------------------------------------- * copy attrs @@ -1027,11 +1043,11 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, /*close */ if (H5Dclose(dset_out) < 0) HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); - }/*!H5T_REFERENCE*/ - }/*h5tools_canreadf*/ + } /* end if not a reference */ + } /* end if h5tools_canreadf (filter availability check) */ /*------------------------------------------------------------------------- - * close + * Close *------------------------------------------------------------------------- */ if (H5Tclose(ftype_id) < 0) @@ -1048,7 +1064,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed"); } /*------------------------------------------------------------------------- - * we do not have request for filter/chunking use H5Ocopy instead + * We do not have request for filter/chunking; use H5Ocopy instead *------------------------------------------------------------------------- */ else { @@ -1080,7 +1096,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed"); /*------------------------------------------------------------------------- - * copy attrs manually + * Copy attrs manually *------------------------------------------------------------------------- */ if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0) @@ -1097,7 +1113,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, if (options->verbose) HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name); - } /* end do we have request for filter/chunking */ + } /* end whether we have request for filter/chunking */ break; /*------------------------------------------------------------------------- @@ -1157,8 +1173,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, default: HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found"); } /* switch */ - } /* end for */ - } /* end if */ + } /* end for each object to traverse */ + } /* end if there are objects */ done: @@ -1196,7 +1212,7 @@ done: HDfree(hslab_buf); return ret_value; -} +} /* end do_copy_objects() */ /*------------------------------------------------------------------------- * Function: print_dataset_info @@ -1290,8 +1306,8 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) default: HDstrcat(strfilter, "UD "); break; - } /* switch */ - }/*i*/ + } /* end switch */ + } /* end for each filter */ if (!pr) HDprintf(FORMAT_OBJ, "dset", objname); @@ -1304,7 +1320,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr) HDstrcat(str, temp); HDprintf(FORMAT_OBJ, str, objname); } -} +} /* end print_dataset_info() */ /*------------------------------------------------------------------------- * Function: copy_user_block @@ -1374,7 +1390,7 @@ done: HDclose(outfid); return ret_value; -} +} /* end copy_user_block() */ /*------------------------------------------------------------------------- * Function: print_user_block @@ -1447,6 +1463,6 @@ done: HDclose(fh); return; -} +} /* end print_user_block() */ #endif |