Merge pull request #1973 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop

* commit 'bc6115931877c6f6d63977f2c03c5e2dbffe3e56':
  HDFFV-10919 merge synching
  HDFFV-10408,10918 Add note

5 files changed, 122 insertions, 234 deletions

diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c
index b1e736a..0579f63 100644
--- a/tools/src/h5dump/h5dump.c
+++ b/tools/src/h5dump/h5dump.c
@@ -1641,8 +1641,7 @@ main(int argc, const char *argv[])
             fid = H5Fopen(fname, H5F_ACC_RDONLY, fapl_id);
         } 
         else {
-            fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT,
-                    driver, NULL, 0);
+            fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, driver, NULL, 0);
         }
 
         if (fid < 0) {
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index 24f4e6c..0183cbf 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -220,11 +220,7 @@ h5repack_addlayout(const char *str, pack_opt_t *options)
  *-------------------------------------------------------------------------
  */
 hid_t
-copy_named_datatype(hid_t          type_in,
-                    hid_t          fidout,
-                    named_dt_t   **named_dt_head_p,
-                    trav_table_t  *travt,
-                    pack_opt_t    *options)
+copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
 {
     named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
     named_dt_t *dt_ret = NULL;         /* Datatype to return */
@@ -248,8 +244,7 @@ copy_named_datatype(hid_t          type_in,
             if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
                 /* Push onto the stack */
                 if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                            "buffer allocation failed failed");
+                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "buffer allocation failed failed");
                 dt->next = *named_dt_head_p;
                 *named_dt_head_p = dt;
 
@@ -289,8 +284,7 @@ copy_named_datatype(hid_t          type_in,
         else
             dt_ret->id_out = H5Tcopy(type_in);
         if (dt_ret->id_out < 0)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                    "H5Tget_native_type-H5Tcopy failed");
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type-H5Tcopy failed");
         if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommit_anon failed");
     } /* end if named datatype not yet in output file */
@@ -347,12 +341,7 @@ done:
  *-------------------------------------------------------------------------
  */
 int
-copy_attr(
-        hid_t          loc_in,
-        hid_t          loc_out,
-        named_dt_t   **named_dt_head_p,
-        trav_table_t  *travt,
-        pack_opt_t    *options)
+copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
 {
     int         ret_value = 0;
     hid_t       attr_id = -1;  /* attr ID */
@@ -382,13 +371,13 @@ copy_attr(
      */
     for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
         /* open attribute */
-        attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT);
-        if (attr_id < 0)
+        if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
 
         if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
 
+        /* get the file datatype  */
         if ((ftype_id = H5Aget_type(attr_id)) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed");
 
@@ -405,8 +394,7 @@ copy_attr(
             /* Copy named dt */
             if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) {
                 H5Fclose(fidout);
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                        "copy_named_datatype failed");
+                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
             }
 
             if (H5Fclose(fidout) < 0)
@@ -425,8 +413,7 @@ copy_attr(
 
         /* get dimensions  */
         if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                    "H5Sget_simple_extent_dims failed");
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
 
         nelmts = 1;
         for (j = 0; j < rank; j++)
@@ -622,8 +609,7 @@ check_options(pack_opt_t *options)
     } /* end for each object in options */
 
     if (options->all_layout == 1 && has_ck)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-            "invalid chunking input: 'all' option is present with other objects");
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid chunking input: 'all' option is present with other objects");
 
     /*-------------------------------------------------------------------------
      * Objects to filter
@@ -669,14 +655,10 @@ check_options(pack_opt_t *options)
             if (options->verbose) {
                 if (pack.filter[j].filtn >= 0) {
                     if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) {
-                        HDprintf(" <%s> with %s filter %d\n", name,
-                                get_sfilter(pack.filter[j].filtn),
-                                pack.filter[j].filtn);
+                        HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn);
                     }
                     else {
-                        HDprintf(" <%s> with %s filter\n",
-                                name,
-                                get_sfilter(pack.filter[j].filtn));
+                        HDprintf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn));
                     }
                 }
             }
@@ -685,9 +667,7 @@ check_options(pack_opt_t *options)
     } /* end for each object in options table */
 
     if (options->all_filter == 1 && has_cp)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                "invalid compression input: 'all' option is present with " \
-                "other objects");
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid compression input: 'all' option is present with other objects");
 
     /*-------------------------------------------------------------------------
      * Check options for the latest format
@@ -695,18 +675,14 @@ check_options(pack_opt_t *options)
      */
 
     if (options->grp_compact < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                "invalid maximum number of links to store as header messages");
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid maximum number of links to store as header messages");
     if (options->grp_indexed < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                "invalid minimum number of links to store in indexed format");
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid minimum number of links to store in the indexed format");
     if (options->grp_indexed > options->grp_compact)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                "minimum indexed size is greater than maximum compact size");
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "minimum indexed size is greater than the maximum compact size");
     for (i = 0; i < 8; i++)
         if (options->msg_size[i] < 0)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                "invalid shared message size");
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid shared message size");
 
     /*------------------------------------------------------------------------
      * Verify new user userblock options; file name must be present
@@ -720,8 +696,7 @@ check_options(pack_opt_t *options)
     }
 
     if (options->ublock_filename == NULL && options->ublock_size != 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                "file name missing for user block", options->ublock_filename);
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file name missing for user block", options->ublock_filename);
 
     /*------------------------------------------------------------------------
      * Verify alignment options; threshold is zero default but alignment not
@@ -729,8 +704,7 @@ check_options(pack_opt_t *options)
      */
 
     if (options->alignment == 0 && options->threshold != 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                "alignment for H5Pset_alignment missing");
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "alignment for H5Pset_alignment missing");
 
 done:
     return ret_value;
@@ -765,8 +739,7 @@ check_objects(const char* fname, pack_opt_t *options)
      *-------------------------------------------------------------------------
      */
     if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR);
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_fopen failed <%s>: %s", fname, H5FOPENERROR);
 
     /*-------------------------------------------------------------------------
      * get the list of objects in the file
@@ -775,6 +748,7 @@ check_objects(const char* fname, pack_opt_t *options)
 
     /* Initialize indexing options */
     h5trav_set_index(sort_by, sort_order);
+    /* init table */
     trav_table_init(&travt);
 
     /* get the list of objects in the file */
@@ -798,8 +772,7 @@ check_objects(const char* fname, pack_opt_t *options)
 
         /* the input object names are present in the file and are valid */
         if (h5trav_getindext(name, travt) < 0)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                    "%s Could not find <%s> in file <%s>. Exiting...\n",
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%s Could not find <%s> in file <%s>. Exiting...\n",
                     (options->verbose ? "\n" : ""), name, fname);
         if (options->verbose)
             HDprintf("...Found\n");
@@ -825,27 +798,21 @@ check_objects(const char* fname, pack_opt_t *options)
                     }
                     else {
                         if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
-                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                                    "H5Dopen2 failed");
+                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
                         if ((sid = H5Dget_space(did)) < 0)
-                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                                    "H5Dget_space failed");
+                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
                         if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
-                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                                    "H5Sget_simple_extent_ndims failed");
+                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
                         HDmemset(dims, 0, sizeof dims);
                         if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
-                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                                    "H5Sget_simple_extent_dims failed");
+                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
                         for (j = 0; j < rank; j++)
                             csize *= dims[j];
                         if (H5Sclose(sid) < 0)
-                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                                    "H5Sclose failed");
+                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
                         if (H5Dclose(did) < 0)
-                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g,
-                                    "H5Dclose failed");
-                    } /* end else (chunk rank is 0) */
+                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
+                    }
 
                     if (csize < ppb) {
                         HDprintf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 398d632..f6409e3 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -37,7 +37,7 @@
  * local functions
  *-------------------------------------------------------------------------
  */
-static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+static int get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
         size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
 static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr);
 static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
@@ -145,8 +145,7 @@ 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++) {
@@ -368,7 +367,7 @@ done:
 } /* end copy_objects() */
 
 /*-------------------------------------------------------------------------
- * Function: Get_hyperslab
+ * Function: get_hyperslab
  *
  * Purpose: Calulate a hyperslab from a dataset for higher performance.
  *          The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
@@ -400,7 +399,7 @@ done:
  *-----------------------------------------*/
 
 int
-Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
         size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
 {
     int     ret_value = 0;
@@ -521,7 +520,7 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
 
 done:
     return ret_value;
-} /* end Get_hyperslab() */
+} /* end get_hyperslab() */
 
 /*-------------------------------------------------------------------------
  * Function: do_copy_objects
@@ -569,7 +568,7 @@ done:
  *  in (2) is that, when using the strip mine size, it assures that the "remaining" part
  *  of the dataset that does not fill an entire strip mine is processed.
  *
- *  1. figure out a hyperslab (dimentions) and size  (refer to Get_hyperslab()).
+ *  1. figure out a hyperslab (dimentions) and size  (refer to get_hyperslab()).
  *  2. Calculate the hyperslab selections as the selection is moving forward.
  *     Selection would be same as the hyperslab except for the remaining edge portion
  *     of the dataset. The code take care of the remaining portion if exist.
@@ -678,11 +677,7 @@ 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)
@@ -799,8 +794,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                         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) {
+                    else if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) {
                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
                     }
 
@@ -847,25 +841,14 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                              * changing to COMPACT. For the reference, COMPACT is limited
                              * by size 64K by library.
                              */
-                            if (options->layout_g != H5D_COMPACT) {
-                                if (size_dset < options->min_comp) {
+                            if (options->layout_g != H5D_COMPACT)
+                                if (size_dset < options->min_comp)
                                     apply_s = 0;
-                                }
-                            }
 
                             /* apply the filter */
-                            if (apply_s) {
-                                if (apply_filters(
-                                        travt->objs[i].name, 
-                                        rank, 
-                                        dims, 
-                                        msize, 
-                                        dcpl_out, 
-                                        options, 
-                                        &has_filter)
-                                    < 0)
+                            if (apply_s)
+                                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 */
@@ -904,36 +887,13 @@ 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 unable to create, retry with original DCPL */
-                            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) {
-                                    HDprintf(" 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)
+                            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");
+                                if (options->verbose)
+                                    HDprintf(" 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)
                                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
                                 apply_f = 0;
                             } /* end if retry dataset create */
@@ -1003,15 +963,9 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                                             dcpl_tmp = dcpl_in; /* reading dataset */
                                     }
 
-                                    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");
+                                    /* get hyperslab dims and size in byte */
+                                    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)
@@ -1033,30 +987,14 @@ 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 {
@@ -1065,25 +1003,12 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                                             hs_select_nelmts = 1;
                                         } /* end (else) 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);
 
@@ -1129,11 +1054,8 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                                 /* print a message that the filter was not applied
                                  * (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_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);
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index db821ef..c628beb 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -237,11 +237,6 @@ static void usage(const char *prog) {
     PRINTVALSTREAM(rawoutstream, "   Using latest file format with maximum compact group size of 10 and\n");
     PRINTVALSTREAM(rawoutstream, "   minimum shared datatype size of 20\n");
     PRINTVALSTREAM(rawoutstream, "\n");
-    PRINTVALSTREAM(rawoutstream, "5) h5repack --low=0 --high=1 file1 file2\n");
-    PRINTVALSTREAM(rawoutstream, "\n");
-    PRINTVALSTREAM(rawoutstream, "   Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via\n");
-    PRINTVALSTREAM(rawoutstream, "   H5Pset_libver_bounds() when creating the repacked file, file2\n");
-    PRINTVALSTREAM(rawoutstream, "\n");
     PRINTVALSTREAM(rawoutstream, "5) h5repack -f SHUF -f GZIP=1 file1 file2\n");
     PRINTVALSTREAM(rawoutstream, "\n");
     PRINTVALSTREAM(rawoutstream, "   Add both filters SHUF and GZIP in this order to all datasets\n");
@@ -250,6 +245,11 @@ static void usage(const char *prog) {
     PRINTVALSTREAM(rawoutstream, "\n");
     PRINTVALSTREAM(rawoutstream, "   Add bzip2 filter to all datasets\n");
     PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "7) h5repack --low=0 --high=1 file1 file2\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "   Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via\n");
+    PRINTVALSTREAM(rawoutstream, "   H5Pset_libver_bounds() when creating the repacked file, file2\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
 }
 
 /*-------------------------------------------------------------------------
diff --git a/tools/src/misc/h5debug.c b/tools/src/misc/h5debug.c
index 96d6b9f..b28457e 100644
--- a/tools/src/misc/h5debug.c
+++ b/tools/src/misc/h5debug.c
@@ -254,7 +254,7 @@ main(int argc, char *argv[])
     uint8_t     sig[H5F_SIGNATURE_LEN];
     size_t      u;
     H5E_auto2_t func;
-    void     *edata;
+    void       *edata;
     hbool_t     api_ctx_pushed = FALSE;             /* Whether API context pushed */
     herr_t      status = SUCCEED;
 
@@ -274,8 +274,8 @@ main(int argc, char *argv[])
     H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
 
     /*
-    * Open the file and get the file descriptor.
-    */
+     * Open the file and get the file descriptor.
+     */
     if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
         HDfprintf(stderr, "cannot create file access property list\n");
         HDexit(1);
@@ -309,8 +309,8 @@ main(int argc, char *argv[])
     }
 
     /*
-    * Parse command arguments.
-    */
+     * Parse command arguments.
+     */
     if(argc > 2)
         addr = (haddr_t)HDstrtoll(argv[2], NULL, 0);
     if(argc > 3)
@@ -323,8 +323,8 @@ main(int argc, char *argv[])
         extra4 = (haddr_t)HDstrtoll(argv[6], NULL, 0);
 
     /*
-    * Read the signature at the specified file position.
-    */
+     * Read the signature at the specified file position.
+     */
     HDfprintf(stdout, "Reading signature at address %a (rel)\n", addr);
     if(H5F_block_read(f, H5FD_MEM_SUPER, addr, sizeof(sig), sig) < 0) {
         HDfprintf(stderr, "cannot read signature\n");
@@ -332,28 +332,28 @@ main(int argc, char *argv[])
     }
     if(!HDmemcmp(sig, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN)) {
         /*
-        * Debug the file's super block.
-        */
+         * Debug the file's super block.
+         */
         status = H5F_debug(f, stdout, 0, VCOL);
 
     } else if(!HDmemcmp(sig, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a local heap.
-        */
+         * Debug a local heap.
+         */
         status = H5HL_debug(f, addr, stdout, 0, VCOL);
 
     }
     else if(!HDmemcmp (sig, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a global heap collection.
-        */
+         * Debug a global heap collection.
+         */
         status = H5HG_debug(f, addr, stdout, 0, VCOL);
 
     }
     else if(!HDmemcmp(sig, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a symbol table node.
-        */
+         * Debug a symbol table node.
+         */
 
         /* Check for extra parameters */
         if(extra == 0) {
@@ -367,10 +367,10 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a B-tree.  B-trees are debugged through the B-tree
-        * subclass.  The subclass identifier is the byte immediately
-        * after the B-tree signature.
-        */
+         * Debug a B-tree.  B-trees are debugged through the B-tree
+         * subclass.  The subclass identifier is the byte immediately
+         * after the B-tree signature.
+         */
         H5B_subid_t subtype = (H5B_subid_t)sig[H5_SIZEOF_MAGIC];
         unsigned    ndims;
         uint32_t    dim[H5O_LAYOUT_NDIMS];
@@ -435,8 +435,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a v2 B-tree header.
-        */
+         * Debug a v2 B-tree header.
+          */
         const H5B2_class_t *cls = get_H5B2_class(sig);
         HDassert(cls);
 
@@ -452,8 +452,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a v2 B-tree internal node.
-        */
+         * Debug a v2 B-tree internal node.
+         */
         const H5B2_class_t *cls = get_H5B2_class(sig);
         HDassert(cls);
 
@@ -479,8 +479,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a v2 B-tree leaf node.
-        */
+         * Debug a v2 B-tree leaf node.
+         */
         const H5B2_class_t *cls = get_H5B2_class(sig);
         HDassert(cls);
 
@@ -505,15 +505,15 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a fractal heap header.
-        */
+         * Debug a fractal heap header.
+         */
         status = H5HF_hdr_debug(f, addr, stdout, 0, VCOL);
 
     }
     else if(!HDmemcmp(sig, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a fractal heap direct block.
-        */
+         * Debug a fractal heap direct block.
+         */
 
         /* Check for enough valid parameters */
         if(extra == 0 || extra2 == 0) {
@@ -528,8 +528,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a fractal heap indirect block.
-        */
+         * Debug a fractal heap indirect block.
+         */
 
         /* Check for enough valid parameters */
         if(extra == 0 || extra2 == 0) {
@@ -544,16 +544,16 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a free space header.
-        */
+         * Debug a free space header.
+         */
 
         status = H5FS_debug(f, addr, stdout, 0, VCOL);
 
     }
     else if(!HDmemcmp(sig, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug free space serialized sections.
-        */
+         * Debug free space serialized sections.
+         */
 
         /* Check for enough valid parameters */
         if(extra == 0 || extra2 == 0) {
@@ -568,16 +568,16 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5SM_TABLE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug shared message master table.
-        */
+         * Debug shared message master table.
+         */
 
         status = H5SM_table_debug(f, addr, stdout, 0, VCOL, (unsigned) UFAIL, (unsigned) UFAIL);
 
     }
     else if(!HDmemcmp(sig, H5SM_LIST_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug shared message list index.
-        */
+         * Debug shared message list index.
+         */
 
         /* Check for enough valid parameters */
         if(extra == 0) {
@@ -592,8 +592,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug an extensible aray header.
-        */
+         * Debug an extensible aray header.
+         */
         const H5EA_class_t *cls = get_H5EA_class(sig);
         HDassert(cls);
 
@@ -610,8 +610,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug an extensible aray index block.
-        */
+         * Debug an extensible aray index block.
+         */
         const H5EA_class_t *cls = get_H5EA_class(sig);
         HDassert(cls);
 
@@ -628,8 +628,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug an extensible aray super block.
-        */
+         * Debug an extensible aray super block.
+         */
         const H5EA_class_t *cls = get_H5EA_class(sig);
         HDassert(cls);
 
@@ -646,8 +646,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug an extensible aray data block.
-        */
+         * Debug an extensible aray data block.
+         */
         const H5EA_class_t *cls = get_H5EA_class(sig);
         HDassert(cls);
 
@@ -664,8 +664,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a fixed array header.
-        */
+         * Debug a fixed array header.
+         */
         const H5FA_class_t *cls = get_H5FA_class(sig);
         HDassert(cls);
 
@@ -682,8 +682,8 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug a fixed array data block.
-        */
+         * Debug a fixed array data block.
+         */
         const H5FA_class_t *cls = get_H5FA_class(sig);
         HDassert(cls);
 
@@ -700,24 +700,24 @@ main(int argc, char *argv[])
     }
     else if(!HDmemcmp(sig, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
         /*
-        * Debug v2 object header (which have signatures).
-        */
+         * Debug v2 object header (which have signatures).
+         */
 
         status = H5O_debug(f, addr, stdout, 0, VCOL);
 
     }
     else if(sig[0] == H5O_VERSION_1) {
         /*
-        * This could be a v1 object header.  Since they don't have a signature
-        * it's a somewhat "ify" detection.
-        */
+         * This could be a v1 object header.  Since they don't have a signature
+         * it's a somewhat "ify" detection.
+         */
         status = H5O_debug(f, addr, stdout, 0, VCOL);
 
     }
     else {
         /*
-        * Got some other unrecognized signature.
-        */
+         * Got some other unrecognized signature.
+         */
         HDprintf("%-*s ", VCOL, "Signature:");
         for (u = 0; u < sizeof(sig); u++) {
             if (sig[u] > ' ' && sig[u] <= '~' && '\\' != sig[u])