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Formatting changes, mostly.

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This commit is contained in:
Jacob Smith 2019-05-30 15:46:39 -05:00
parent a648183cc3
commit cb6029196a
1 changed files with 124 additions and 57 deletions
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181
tools/src/h5repack/h5repack_copy.c
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@ -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;
@ -387,7 +387,7 @@ done:
trav_table_free(travt);
return ret_value;
}
} /* end copy_objects() */
/*-------------------------------------------------------------------------
* Function: Get_hyperslab
@ -543,7 +543,7 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
done:
return ret_value;
}
} /* end Get_hyperslab() */
/*-------------------------------------------------------------------------
* Function: do_copy_objects
@ -599,7 +599,8 @@ 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;
@ -699,7 +700,11 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
}
else {
if (options->grp_compact > 0 || options->grp_indexed > 0)
if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0)
if (H5Pset_link_phase_change(
gcpl_out,
(unsigned) options->grp_compact,
(unsigned) options->grp_indexed)
< 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed");
if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
@ -780,6 +785,9 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (H5Dclose(dset_in) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
/* TODO: be smart about external storage */
/* can we use the dcpl_in/out to adjust any external storage? */
/* what about the case with just H5Ocopy? */
/*-------------------------------------------------------------------------
* check if we should use H5Ocopy or not
* if there is a request for filters/layout, we read/write the object
@ -819,7 +827,7 @@ 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");
@ -858,12 +866,20 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
/* apply the filter */
if (apply_s)
if (apply_filters(travt->objs[i].name, rank, dims, msize, dcpl_out, options, &has_filter) < 0)
if (apply_filters(
travt->objs[i].name,
rank,
dims,
msize,
dcpl_out,
options,
&has_filter)
< 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed");
/* 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
@ -883,14 +899,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
/* if convert to COMPACT */
if (options->layout_g == H5D_COMPACT)
/* should be smaller than 64K */
if (size_dset > MAX_COMPACT_DSIZE)
limit_maxdims = FALSE;
/* unset unlimited max dims */
if (limit_maxdims)
H5Sset_extent_simple(f_space_id, rank, dims, NULL);
}
} /* if not chunked */
} /* if layout change requested for entire file or individual object */
/*-------------------------------------------------------------------------
* create the output dataset;
@ -898,16 +914,36 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
* modified dcpl; in that case use the original instead
*-------------------------------------------------------------------------
*/
dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
if (dset_out == FAIL) {
H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
dset_out = H5Dcreate2(fidout,
travt->objs[i].name,
wtype_id,
f_space_id,
H5P_DEFAULT,
dcpl_out,
H5P_DEFAULT);
if (dset_out < 0) {
H5Epush2(H5tools_ERR_STACK_g,
__FILE__,
FUNC,
__LINE__,
H5tools_ERR_CLS_g,
H5E_tools_g,
H5E_tools_min_id_g,
"H5Dcreate2 failed");
if (options->verbose)
printf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name);
if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
printf(" warning: could not create dataset <%s>. Applying original settings\n",
travt->objs[i].name);
dset_out = H5Dcreate2(fidout,
travt->objs[i].name,
wtype_id,
f_space_id,
H5P_DEFAULT,
dcpl_in,
H5P_DEFAULT);
if (dset_out < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
apply_f = 0;
}
} /* if opening dataset with original DCPL (retry) */
/*-------------------------------------------------------------------------
* read/write
@ -931,8 +967,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
/* free */
if (buf != NULL) {
if (buf != NULL) { /* TODO: is buf potentially released by H5Dvlen_reclaim()? */
HDfree(buf);
buf = NULL;
}
@ -968,17 +1004,25 @@ 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 */
}
/* get hyperslab dims and size in byte */
if (Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
if (Get_hyperslab(
dcpl_tmp,
rank,
dims,
p_type_nbytes,
hslab_dims,
&hslab_nbytes)
< 0)
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);
@ -996,28 +1040,57 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*/
for (k = 0, hs_select_nelmts = 1; k < rank; k++) {
/* MIN() is used to get the remaining edge portion if exist.
* "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
* "dims[k] - hs_sel_offset[k]" is remaining edge portion that is
* smaller then the hyperslab.
*/
hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
hs_select_nelmts *= hs_sel_count[k];
}
if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
if (H5Sselect_hyperslab(
f_space_id,
H5S_SELECT_SET,
hs_sel_offset,
NULL,
hs_sel_count,
NULL)
< 0)
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)
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 */
} /* rank == 0 */
if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 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");
if(H5Dwrite(dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
if (H5Dwrite(
dset_out,
wtype_id,
hslab_space,
f_space_id,
H5P_DEFAULT,
hslab_buf)
< 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
/* reclaim any VL memory, if necessary */
if (vl_data)
H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
@ -1029,20 +1102,19 @@ 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 */
}
} /* hyperslab selection loop */
H5Sclose(hslab_space);
/* free */
if (hslab_buf != NULL) {
HDfree(hslab_buf);
hslab_buf = NULL;
}
} /* hyperslab read */
} /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
} /* end if reading/writing by hyperslab */
} /* if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) */
/*-------------------------------------------------------------------------
* amount of compression used
* print amount of compression used
*-------------------------------------------------------------------------
*/
if (options->verbose) {
@ -1062,14 +1134,16 @@ 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)
printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp);
printf(" <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)
printf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name);
} /* verbose */
} /* if verbose (print compression) */
/*-------------------------------------------------------------------------
* copy attrs
@ -1078,11 +1152,10 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
/*close */
if (H5Dclose(dset_out) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
}/*!H5T_REFERENCE*/
}/*h5tools_canreadf*/
} /* !H5T_REFERENCE */
} /* if h5tools_canreadf (filter availability check) */
/*-------------------------------------------------------------------------
* close
@ -1116,11 +1189,6 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed");
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------
*/
if (H5Ocopy(fidin, /* Source file or group identifier */
travt->objs[i].name, /* Name of the source object to be copied */
fidout, /* Destination file or group identifier */
@ -1129,7 +1197,6 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed");
/* close property */
if (H5Pclose(pid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
@ -1151,7 +1218,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (options->verbose)
printf(FORMAT_OBJ, "dset", travt->objs[i].name);
} /* end do we have request for filter/chunking */
} /* end whether we have request for filter/chunking */
break;
/*-------------------------------------------------------------------------
@ -1211,8 +1278,8 @@ 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:
@ -1250,7 +1317,7 @@ done:
HDfree(hslab_buf);
return ret_value;
}
} /* end do_copy_objects() */
/*-------------------------------------------------------------------------
* Function: print_dataset_info
@ -1345,7 +1412,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
HDstrcat(strfilter, "UD ");
break;
} /* switch */
}/*i*/
} /* for each filter */
if (!pr)
printf(FORMAT_OBJ, "dset", objname);
@ -1358,7 +1425,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
HDstrcat(str, temp);
printf(FORMAT_OBJ, str, objname);
}
}
} /* end print_dataset_info() */
/*-------------------------------------------------------------------------
* Function: copy_user_block
@ -1428,7 +1495,7 @@ done:
HDclose(outfid);
return ret_value;
}
} /* end copy_user_block() */
/*-------------------------------------------------------------------------
* Function: print_user_block
@ -1501,6 +1568,6 @@ done:
HDclose(fh);
return;
}
} /* end print_user_block() */
#endif