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Diffstat (limited to 'tools/h5repack/h5repack_copy.c')
-rw-r--r--tools/h5repack/h5repack_copy.c108
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
generated by cgit v0.12 at 2024-10-30 02:20:37 (GMT)