Brings over most of the HD prefix removal (#3293)

6 files changed, 238 insertions, 239 deletions

diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index c58943b..0ced980 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -71,7 +71,7 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest)
 {
     int k, n;
 
-    HDmemset(options, 0, sizeof(pack_opt_t));
+    memset(options, 0, sizeof(pack_opt_t));
     options->min_comp   = 0;
     options->verbose    = verbose;
     options->latest     = latest;
@@ -132,7 +132,7 @@ h5repack_addfilter(const char *str, pack_opt_t *options)
         n = options->n_filter_g++; /* increase # of global filters */
         if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) {
             error_msg("maximum number of filters exceeded for <%s>\n", str);
-            HDfree(obj_list);
+            free(obj_list);
             return -1;
         }
 
@@ -141,7 +141,7 @@ h5repack_addfilter(const char *str, pack_opt_t *options)
     else
         options_add_filter(obj_list, n_objs, filter, options->op_tbl);
 
-    HDfree(obj_list);
+    free(obj_list);
     return 0;
 } /* end h5repack_addfilter() */
 
@@ -195,7 +195,7 @@ h5repack_addlayout(const char *str, pack_opt_t *options)
         if (options->all_layout == 0)
             ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl);
 
-        HDfree(obj_list);
+        free(obj_list);
         ret_value = 0;
     } /* end if obj_list exists */
 
@@ -253,13 +253,13 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t
         for (i = 0; i < travt->nobjs; i++) {
             if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
                 /* Push onto the stack */
-                if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
+                if (NULL == (dt = (named_dt_t *)malloc(sizeof(named_dt_t))))
                     H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed");
                 dt->next         = *named_dt_head_p;
                 *named_dt_head_p = dt;
 
                 /* Update the token/address and id */
-                HDmemcpy(&dt->obj_token, &travt->objs[i].obj_token, sizeof(H5O_token_t));
+                memcpy(&dt->obj_token, &travt->objs[i].obj_token, sizeof(H5O_token_t));
                 dt->id_out = H5I_INVALID_HID;
 
                 /* Check if this type is the one requested */
@@ -276,13 +276,13 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t
      */
     if (!dt_ret) {
         /* Push the new datatype onto the stack */
-        if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
+        if (NULL == (dt_ret = (named_dt_t *)malloc(sizeof(named_dt_t))))
             H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "buffer allocation failed failed");
         dt_ret->next     = *named_dt_head_p;
         *named_dt_head_p = dt_ret;
 
         /* Update the token/address and id */
-        HDmemcpy(&dt_ret->obj_token, &oinfo.token, sizeof(H5O_token_t));
+        memcpy(&dt_ret->obj_token, &oinfo.token, sizeof(H5O_token_t));
         dt_ret->id_out = H5I_INVALID_HID;
     } /* end if requested datatype not found */
 
@@ -330,7 +330,7 @@ named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
         if (H5Tclose(dt->id_out) < 0 && !ignore_err)
             H5TOOLS_GOTO_ERROR((-1), "H5Tclose failed");
         dt = dt->next;
-        HDfree(*named_dt_head_p);
+        free(*named_dt_head_p);
         *named_dt_head_p = dt;
     }
 
@@ -481,9 +481,9 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_
              *-----------------------------------------------------------------
              */
 
-            buf = (void *)HDmalloc((size_t)(nelmts * msize));
+            buf = (void *)malloc((size_t)(nelmts * msize));
             if (buf == NULL) {
-                H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed");
+                H5TOOLS_GOTO_ERROR((-1), "malloc failed");
             } /* end if */
             if (options->verbose == 2) {
                 H5_timer_init(&timer);
@@ -526,15 +526,15 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_
             if (TRUE == h5tools_detect_vlen(wtype_id))
                 H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf);
 
-            HDfree(buf);
+            free(buf);
             buf = NULL;
         } /*H5T_REFERENCE*/
 
         if (options->verbose > 0) {
             if (options->verbose == 2)
-                HDprintf(FORMAT_OBJ_ATTR_TIME, "attr", read_time, write_time, name);
+                printf(FORMAT_OBJ_ATTR_TIME, "attr", read_time, write_time, name);
             else
-                HDprintf(FORMAT_OBJ_ATTR, "attr", name);
+                printf(FORMAT_OBJ_ATTR, "attr", name);
         }
 
         /*---------------------------------------------------------------------
@@ -566,7 +566,7 @@ done:
                 H5Treclaim(wtype_id, space_id, H5P_DEFAULT, buf);
 
             /* Free buf */
-            HDfree(buf);
+            free(buf);
         }
 
         H5Aclose(attr_out);
@@ -602,7 +602,7 @@ check_options(pack_opt_t *options)
      */
     if (options->verbose > 0 && have_request(options)) {
         if (options->all_layout == 1) {
-            HDprintf("All objects to modify layout are...\n");
+            printf("All objects to modify layout are...\n");
             switch (options->layout_g) {
                 case H5D_COMPACT:
                     strcpy(slayout, "compact");
@@ -624,17 +624,17 @@ check_options(pack_opt_t *options)
                     strcpy(slayout, "invalid layout\n");
                     H5TOOLS_GOTO_DONE((-1));
             }
-            HDprintf(" Apply %s layout to all", slayout);
+            printf(" Apply %s layout to all", slayout);
             if (H5D_CHUNKED == options->layout_g) {
-                HDprintf("with dimension [ ");
+                printf("with dimension [ ");
                 for (j = 0; j < options->chunk_g.rank; j++)
-                    HDprintf("%d ", (int)options->chunk_g.chunk_lengths[j]);
-                HDprintf("]");
+                    printf("%d ", (int)options->chunk_g.chunk_lengths[j]);
+                printf("]");
             }
-            HDprintf("\n");
+            printf("\n");
         }
         else
-            HDprintf("No all objects to modify layout\n");
+            printf("No all objects to modify layout\n");
     } /* end if verbose */
 
     for (i = 0; i < options->op_tbl->nelems; i++) {
@@ -642,16 +642,16 @@ check_options(pack_opt_t *options)
 
         if (options->op_tbl->objs[i].chunk.rank > 0) {
             if (options->verbose > 0) {
-                HDprintf(" <%s> with chunk size ", name);
+                printf(" <%s> with chunk size ", name);
                 for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
-                    HDprintf("%d ", (int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
-                HDprintf("\n");
+                    printf("%d ", (int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
+                printf("\n");
             }
             has_ck = 1;
         }
         else if (options->op_tbl->objs[i].chunk.rank == -2) { /* TODO: replace 'magic number' */
             if (options->verbose > 0)
-                HDprintf(" <%s> %s\n", name, "NONE (contiguous)");
+                printf(" <%s> %s\n", name, "NONE (contiguous)");
             has_ck = 1;
         }
     } /* end for each object in options */
@@ -666,34 +666,34 @@ check_options(pack_opt_t *options)
 
     if (options->verbose > 0 && have_request(options)) {
         if (options->all_filter == 1) {
-            HDprintf("All objects to apply filter are...\n");
+            printf("All objects to apply filter are...\n");
             for (k = 0; k < options->n_filter_g; k++) {
                 H5Z_filter_t filtn = options->filter_g[k].filtn;
                 if (filtn < 0) {
-                    HDprintf(" Unknown\n");
+                    printf(" Unknown\n");
                     continue;
                 }
                 switch (filtn) {
                     case H5Z_FILTER_NONE:
-                        HDprintf(" Uncompress all\n");
+                        printf(" Uncompress all\n");
                         break;
                     case H5Z_FILTER_SHUFFLE:
                     case H5Z_FILTER_FLETCHER32:
-                        HDprintf(" All with %s\n", get_sfilter(filtn));
+                        printf(" All with %s\n", get_sfilter(filtn));
                         break;
                     case H5Z_FILTER_SZIP:
                     case H5Z_FILTER_DEFLATE:
-                        HDprintf(" All with %s, parameter %d\n", get_sfilter(filtn),
-                                 options->filter_g[k].cd_values[0]);
+                        printf(" All with %s, parameter %d\n", get_sfilter(filtn),
+                               options->filter_g[k].cd_values[0]);
                         break;
                     default:
-                        HDprintf(" User Defined %d\n", filtn);
+                        printf(" User Defined %d\n", filtn);
                         break;
                 } /* end switch */
             }     /* end for each filter */
         }         /* end if options->all_filter == 1 (TODO: meaning) */
         else
-            HDprintf("No all objects to apply filter\n");
+            printf("No all objects to apply filter\n");
     } /* end if verbose */
 
     for (i = 0; i < options->op_tbl->nelems; i++) {
@@ -704,11 +704,11 @@ check_options(pack_opt_t *options)
             if (options->verbose > 0) {
                 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);
+                        printf(" <%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));
+                        printf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn));
                     }
                 }
             }
@@ -740,8 +740,8 @@ check_options(pack_opt_t *options)
      */
     if (options->ublock_filename != NULL && options->ublock_size == 0) {
         if (options->verbose > 0) {
-            HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
-                     options->ublock_filename);
+            printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
+                   options->ublock_filename);
             options->ublock_size = 1024;
         }
     }
@@ -813,21 +813,21 @@ check_objects(const char *fname, pack_opt_t *options)
      */
 
     if (options->verbose > 0)
-        HDprintf("Opening file. Searching %zu objects to modify ...\n", travt->nobjs);
+        printf("Opening file. Searching %zu objects to modify ...\n", travt->nobjs);
 
     for (i = 0; i < options->op_tbl->nelems; i++) {
         pack_info_t obj  = options->op_tbl->objs[i];
         char       *name = obj.path;
 
         if (options->verbose > 0)
-            HDprintf(" <%s>", name);
+            printf(" <%s>", name);
 
         /* the input object names are present in the file and are valid */
         if (h5trav_getindext(name, travt) < 0)
             H5TOOLS_GOTO_ERROR((-1), "%s Could not find <%s> in file <%s>. Exiting...\n",
                                (options->verbose > 0 ? "\n" : ""), name, fname);
         if (options->verbose > 0)
-            HDprintf("...Found\n");
+            printf("...Found\n");
 
         for (ifil = 0; ifil < obj.nfilters; ifil++) {
             if (obj.filter[ifil].filtn < 0)
@@ -854,7 +854,7 @@ check_objects(const char *fname, pack_opt_t *options)
                             H5TOOLS_GOTO_ERROR((-1), "H5Dget_space failed");
                         if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
                             H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed");
-                        HDmemset(dims, 0, sizeof dims);
+                        memset(dims, 0, sizeof dims);
                         if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
                             H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed");
                         for (j = 0; j < rank; j++)
@@ -866,7 +866,7 @@ check_objects(const char *fname, pack_opt_t *options)
                     }
 
                     if (csize < ppb) {
-                        HDprintf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
+                        printf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
                         H5TOOLS_GOTO_DONE(0);
                     }
                 } /* end case SZIP */
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 42c393b..172ba26 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -299,7 +299,7 @@ copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options)
      *-------------------------------------------------------------------------
      */
     if (options->verbose > 0)
-        HDprintf("Making new file ...\n");
+        printf("Making new file ...\n");
 
     if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, options->fout_fapl)) < 0)
         H5TOOLS_GOTO_ERROR((-1), "H5Fcreate could not create file <%s>:", fnameout);
@@ -658,7 +658,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
     int                ret_value = 0;
 
     /* init linkinfo struct */
-    HDmemset(&linkinfo, 0, sizeof(h5tool_link_info_t));
+    memset(&linkinfo, 0, sizeof(h5tool_link_info_t));
 
     /*-------------------------------------------------------------------------
      * copy the supplied object list
@@ -667,14 +667,14 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
 
     if (options->verbose > 0) {
         if (options->verbose == 2) {
-            HDprintf("-----------------------------------------------------------------\n");
-            HDprintf(" Type     Filter (Compression)        Timing read/write    Name\n");
-            HDprintf("-----------------------------------------------------------------\n");
+            printf("-----------------------------------------------------------------\n");
+            printf(" Type     Filter (Compression)        Timing read/write    Name\n");
+            printf("-----------------------------------------------------------------\n");
         }
         else {
-            HDprintf("-----------------------------------------\n");
-            HDprintf(" Type     Filter (Compression)     Name\n");
-            HDprintf("-----------------------------------------\n");
+            printf("-----------------------------------------\n");
+            printf(" Type     Filter (Compression)     Name\n");
+            printf("-----------------------------------------\n");
         }
     }
 
@@ -695,9 +695,9 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                 case H5TRAV_TYPE_GROUP:
                     if (options->verbose > 0) {
                         if (options->verbose == 2)
-                            HDprintf(FORMAT_OBJ_NOTIME, "group", travt->objs[i].name);
+                            printf(FORMAT_OBJ_NOTIME, "group", travt->objs[i].name);
                         else
-                            HDprintf(FORMAT_OBJ, "group", travt->objs[i].name);
+                            printf(FORMAT_OBJ, "group", travt->objs[i].name);
                     }
 
                     /* open input group */
@@ -877,7 +877,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                             H5TOOLS_GOTO_ERROR((-1), "H5Dget_create_plist failed");
                         if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
                             H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_ndims failed");
-                        HDmemset(dims, 0, sizeof dims);
+                        memset(dims, 0, sizeof dims);
                         if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
                             H5TOOLS_GOTO_ERROR((-1), "H5Sget_simple_extent_dims failed");
                         if (H5Dget_space_status(dset_in, &space_status) < 0)
@@ -991,9 +991,9 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                 if (dset_out == H5I_INVALID_HID) {
                                     H5TOOLS_INFO("H5Dcreate2 failed");
                                     if (options->verbose > 0)
-                                        HDprintf(" warning: could not create dataset <%s>. Applying original "
-                                                 "settings\n",
-                                                 travt->objs[i].name);
+                                        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,
@@ -1012,7 +1012,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                     /* have to read the whole dataset if there is only one element in the
                                      * dataset */
                                     if (need < H5TOOLS_MALLOCSIZE)
-                                        buf = HDmalloc(need);
+                                        buf = malloc(need);
 
                                     /* Set up collective write if using filters in parallel */
                                     {
@@ -1061,7 +1061,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
 
                                         if (buf != NULL) { /* TODO: is buf potentially released by
                                                               H5Dvlen_reclaim()? */
-                                            HDfree(buf);
+                                            free(buf);
                                             buf = NULL;
                                         }
                                     }
@@ -1108,7 +1108,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                                           &hslab_nbytes) < 0)
                                             H5TOOLS_GOTO_ERROR((-1), "get_hyperslab failed");
 
-                                        hslab_buf = HDmalloc((size_t)hslab_nbytes);
+                                        hslab_buf = malloc((size_t)hslab_nbytes);
                                         if (hslab_buf == NULL)
                                             H5TOOLS_GOTO_ERROR((-1), "can't allocate space for hyperslab");
 
@@ -1116,8 +1116,8 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                         hslab_space  = H5Screate_simple(1, &hslab_nelmts, NULL);
 
                                         /* the hyperslab selection loop */
-                                        HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset);
-                                        HDmemset(zero, 0, sizeof zero);
+                                        memset(hs_sel_offset, 0, sizeof hs_sel_offset);
+                                        memset(zero, 0, sizeof zero);
 
                                         for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) {
                                             if (rank > 0) {
@@ -1189,7 +1189,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
 
                                         H5Sclose(hslab_space);
                                         if (hslab_buf != NULL) {
-                                            HDfree(hslab_buf);
+                                            free(hslab_buf);
                                             hslab_buf = NULL;
                                         }
                                     } /* end if reading/writing by hyperslab */
@@ -1221,13 +1221,13 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                      * (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);
+                                        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)
-                                        HDprintf(" <warning: could not apply the filter to %s>\n",
-                                                 travt->objs[i].name);
+                                        printf(" <warning: could not apply the filter to %s>\n",
+                                               travt->objs[i].name);
                                 } /* end if verbose (print compression) */
 
                                 /*-------------------------------------------------------------------------
@@ -1310,9 +1310,9 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
 
                         if (options->verbose > 0) {
                             if (options->verbose == 2)
-                                HDprintf(FORMAT_OBJ_TIME, "dset", 0.0, write_time, travt->objs[i].name);
+                                printf(FORMAT_OBJ_TIME, "dset", 0.0, write_time, travt->objs[i].name);
                             else
-                                HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name);
+                                printf(FORMAT_OBJ, "dset", travt->objs[i].name);
                         }
 
                     } /* end whether we have request for filter/chunking */
@@ -1327,9 +1327,9 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                 case H5TRAV_TYPE_NAMED_DATATYPE:
                     if (options->verbose > 0) {
                         if (options->verbose == 2)
-                            HDprintf(FORMAT_OBJ_NOTIME, "type", travt->objs[i].name);
+                            printf(FORMAT_OBJ_NOTIME, "type", travt->objs[i].name);
                         else
-                            HDprintf(FORMAT_OBJ, "type", travt->objs[i].name);
+                            printf(FORMAT_OBJ, "type", travt->objs[i].name);
                     }
 
                     if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
@@ -1371,9 +1371,9 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                 case H5TRAV_TYPE_UDLINK:
                     if (options->verbose > 0) {
                         if (options->verbose == 2)
-                            HDprintf(FORMAT_OBJ_NOTIME, "link", travt->objs[i].name);
+                            printf(FORMAT_OBJ_NOTIME, "link", travt->objs[i].name);
                         else
-                            HDprintf(FORMAT_OBJ, "link", travt->objs[i].name);
+                            printf(FORMAT_OBJ, "link", travt->objs[i].name);
                     }
 
                     /* Check -X option. */
@@ -1381,7 +1381,7 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                         if (H5tools_get_symlink_info(fidin, travt->objs[i].name, &linkinfo, 1) == 0) {
                             /* dangling link */
                             if (options->prune) {
-                                HDprintf("Pruned %s.\n", travt->objs[i].name);
+                                printf("Pruned %s.\n", travt->objs[i].name);
                             }
                             else {
                                 if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name,
@@ -1421,12 +1421,12 @@ do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
 
                         /* free link info path */
                         if (linkinfo.trg_path)
-                            HDfree(linkinfo.trg_path);
+                            free(linkinfo.trg_path);
                         linkinfo.trg_path = NULL;
                     } /* options->merge */
                     else {
                         if (options->prune) {
-                            HDprintf("Pruned %s.\n", travt->objs[i].name);
+                            printf("Pruned %s.\n", travt->objs[i].name);
                         }
                         else {
                             if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT,
@@ -1460,7 +1460,7 @@ done:
 
     /* free link info path */
     if (linkinfo.trg_path)
-        HDfree(linkinfo.trg_path);
+        free(linkinfo.trg_path);
 
     H5E_BEGIN_TRY
     {
@@ -1484,9 +1484,9 @@ done:
 
     /* free */
     if (buf != NULL)
-        HDfree(buf);
+        free(buf);
     if (hslab_buf != NULL)
-        HDfree(hslab_buf);
+        free(hslab_buf);
 
     return ret_value;
 } /* end do_copy_objects() */
@@ -1589,9 +1589,9 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr, pack_opt_
 
     if (!pr)
         if (options->verbose == 2)
-            HDprintf(FORMAT_OBJ_TIME, "dset", read_time, write_time, objname);
+            printf(FORMAT_OBJ_TIME, "dset", read_time, write_time, objname);
         else
-            HDprintf(FORMAT_OBJ, "dset", objname);
+            printf(FORMAT_OBJ, "dset", objname);
     else {
         char str[512], temp[512];
 
@@ -1600,9 +1600,9 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr, pack_opt_
         HDsnprintf(temp, sizeof(temp), "  (%.3f:1)", ratio);
         HDstrcat(str, temp);
         if (options->verbose == 2)
-            HDprintf(FORMAT_OBJ_TIME, str, read_time, write_time, objname);
+            printf(FORMAT_OBJ_TIME, str, read_time, write_time, objname);
         else
-            HDprintf(FORMAT_OBJ, str, objname);
+            printf(FORMAT_OBJ, str, objname);
     }
 } /* end print_dataset_info() */
 
@@ -1654,13 +1654,13 @@ copy_user_block(const char *infile, const char *outfile, hsize_t size)
             } while (-1 == nwritten && EINTR == errno);
             if (-1 == nwritten) /* error */
                 H5TOOLS_GOTO_ERROR((-1), "HDwrite failed");
-            HDassert(nwritten > 0);
-            HDassert(nwritten <= nbytes);
+            assert(nwritten > 0);
+            assert(nwritten <= nbytes);
 
             /* Update # of bytes left & offset in buffer */
             nbytes -= nwritten;
             wbuf += nwritten;
-            HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
+            assert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
         } /* end while */
 
         /* Update size of userblock left to transfer */
@@ -1728,9 +1728,9 @@ print_user_block(const char *filename, hid_t fid)
 
         for (i = 0; i < nread; i++) {
 
-            HDprintf("%c ", rbuf[i]);
+            printf("%c ", rbuf[i]);
         }
-        HDprintf("\n");
+        printf("\n");
 
         if (nread < 0) {
             H5TOOLS_GOTO_ERROR((-1), "nread < 0");
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index 5ecb423..0621c7a 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -370,7 +370,7 @@ static void
 leave(int ret)
 {
     h5tools_close();
-    HDexit(ret);
+    exit(ret);
 }
 
 /*-------------------------------------------------------------------------
@@ -391,7 +391,7 @@ read_info(const char *filename, pack_opt_t *options)
     int   i;
     int   ret_value = EXIT_SUCCESS;
 
-    if (NULL == (fp = HDfopen(filename, "r"))) {
+    if (NULL == (fp = fopen(filename, "r"))) {
         error_msg("cannot open options file %s\n", filename);
         h5tools_setstatus(EXIT_FAILURE);
         ret_value = EXIT_FAILURE;
@@ -534,10 +534,10 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
     int                ret_value = 0;
 
     /* Initialize fapl info structs */
-    HDmemset(&in_vol_info, 0, sizeof(h5tools_vol_info_t));
-    HDmemset(&out_vol_info, 0, sizeof(h5tools_vol_info_t));
-    HDmemset(&in_vfd_info, 0, sizeof(h5tools_vfd_info_t));
-    HDmemset(&out_vfd_info, 0, sizeof(h5tools_vfd_info_t));
+    memset(&in_vol_info, 0, sizeof(h5tools_vol_info_t));
+    memset(&out_vol_info, 0, sizeof(h5tools_vol_info_t));
+    memset(&in_vfd_info, 0, sizeof(h5tools_vfd_info_t));
+    memset(&out_vfd_info, 0, sizeof(h5tools_vfd_info_t));
 
     /* parse command line options */
     while (EOF != (opt = H5_get_option(argc, argv, s_opts, l_opts))) {
@@ -569,7 +569,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
 
             case 'v':
                 if (H5_optarg != NULL) {
-                    if (2 == HDatoi(H5_optarg))
+                    if (2 == atoi(H5_optarg))
                         options->verbose = 2;
                 }
                 else
@@ -624,7 +624,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
                 break;
 
             case 'j':
-                bound = HDatoi(H5_optarg);
+                bound = atoi(H5_optarg);
                 if (bound < H5F_LIBVER_EARLIEST || bound > H5F_LIBVER_LATEST) {
                     error_msg("in parsing low bound\n");
                     h5tools_setstatus(EXIT_FAILURE);
@@ -635,7 +635,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
                 break;
 
             case 'k':
-                bound = HDatoi(H5_optarg);
+                bound = atoi(H5_optarg);
                 if (bound < H5F_LIBVER_EARLIEST || bound > H5F_LIBVER_LATEST) {
                     error_msg("in parsing high bound\n");
                     h5tools_setstatus(EXIT_FAILURE);
@@ -654,13 +654,13 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
                 break;
 
             case 'c':
-                options->grp_compact = HDatoi(H5_optarg);
+                options->grp_compact = atoi(H5_optarg);
                 if (options->grp_compact > 0)
                     options->latest = TRUE; /* must use latest format */
                 break;
 
             case 'd':
-                options->grp_indexed = HDatoi(H5_optarg);
+                options->grp_indexed = atoi(H5_optarg);
                 if (options->grp_indexed > 0)
                     options->latest = TRUE; /* must use latest format */
                 break;
@@ -671,7 +671,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
                 char *msgPtr    = HDstrchr(H5_optarg, ':');
                 options->latest = TRUE; /* must use latest format */
                 if (msgPtr == NULL) {
-                    ssize = HDatoi(H5_optarg);
+                    ssize = atoi(H5_optarg);
                     for (idx = 0; idx < 5; idx++)
                         options->msg_size[idx] = ssize;
                 }
@@ -680,7 +680,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
 
                     HDstrcpy(msgType, msgPtr + 1);
                     msgPtr[0] = '\0';
-                    ssize     = HDatoi(H5_optarg);
+                    ssize     = atoi(H5_optarg);
                     if (!HDstrncmp(msgType, "dspace", 6))
                         options->msg_size[0] = ssize;
                     else if (!HDstrncmp(msgType, "dtype", 5))
@@ -744,7 +744,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
             } break;
 
             case 'P':
-                options->fs_persist = HDatoi(H5_optarg);
+                options->fs_persist = atoi(H5_optarg);
                 if (options->fs_persist == 0)
                     /* To distinguish the "specified" zero value */
                     options->fs_persist = -1;
@@ -784,14 +784,14 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
 
             case 'E':
                 if (H5_optarg != NULL)
-                    enable_error_stack = HDatoi(H5_optarg);
+                    enable_error_stack = atoi(H5_optarg);
                 else
                     enable_error_stack = 1;
                 break;
 
             case '1':
                 in_vol_info.type    = VOL_BY_VALUE;
-                in_vol_info.u.value = (H5VL_class_value_t)HDatoi(H5_optarg);
+                in_vol_info.u.value = (H5VL_class_value_t)atoi(H5_optarg);
                 custom_in_vol       = TRUE;
                 break;
 
@@ -807,7 +807,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
 
             case '4':
                 out_vol_info.type    = VOL_BY_VALUE;
-                out_vol_info.u.value = (H5VL_class_value_t)HDatoi(H5_optarg);
+                out_vol_info.u.value = (H5VL_class_value_t)atoi(H5_optarg);
                 custom_out_vol       = TRUE;
                 break;
 
@@ -823,7 +823,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
 
             case '7':
                 in_vfd_info.type    = VFD_BY_VALUE;
-                in_vfd_info.u.value = (H5FD_class_value_t)HDatoi(H5_optarg);
+                in_vfd_info.u.value = (H5FD_class_value_t)atoi(H5_optarg);
                 custom_in_vfd       = TRUE;
                 break;
 
@@ -839,7 +839,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
 
             case '0':
                 out_vfd_info.type    = VFD_BY_VALUE;
-                out_vfd_info.u.value = (H5FD_class_value_t)HDatoi(H5_optarg);
+                out_vfd_info.u.value = (H5FD_class_value_t)atoi(H5_optarg);
                 custom_out_vfd       = TRUE;
                 break;
 
@@ -891,7 +891,7 @@ parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
             errno                      = 0;
             onion_fa_in_g.revision_num = HDstrtoull(in_vfd_info.info, NULL, 10);
             if (errno == ERANGE) {
-                HDprintf("Invalid onion revision specified for the input file\n");
+                printf("Invalid onion revision specified for the input file\n");
                 usage(h5tools_getprogname());
                 exit(EXIT_FAILURE);
             }
@@ -965,7 +965,7 @@ main(int argc, char **argv)
     pack_opt_t options; /*the global options */
     int        parse_ret;
 
-    HDmemset(&options, 0, sizeof(pack_opt_t));
+    memset(&options, 0, sizeof(pack_opt_t));
 
     /* Initialize h5tools lib */
     h5tools_init();
@@ -975,14 +975,14 @@ main(int argc, char **argv)
 
     /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */
     if (h5tools_getenv_update_hyperslab_bufsize() < 0) {
-        HDprintf("Error occurred while retrieving H5TOOLS_BUFSIZE value\n");
+        printf("Error occurred while retrieving H5TOOLS_BUFSIZE value\n");
         h5tools_setstatus(EXIT_FAILURE);
         goto done;
     }
 
     /* initialize options  */
     if (h5repack_init(&options, 0, FALSE) < 0) {
-        HDprintf("Error occurred while initializing repack options\n");
+        printf("Error occurred while initializing repack options\n");
         h5tools_setstatus(EXIT_FAILURE);
         goto done;
     }
@@ -992,7 +992,7 @@ main(int argc, char **argv)
 
     parse_ret = parse_command_line(argc, (const char *const *)argv, &options);
     if (parse_ret < 0) {
-        HDprintf("Error occurred while parsing command-line options\n");
+        printf("Error occurred while parsing command-line options\n");
         h5tools_setstatus(EXIT_FAILURE);
         goto done;
     }
@@ -1007,7 +1007,7 @@ main(int argc, char **argv)
 
     /* pack it */
     if (h5repack(infile, outfile, &options) < 0) {
-        HDprintf("Error occurred while repacking\n");
+        printf("Error occurred while repacking\n");
         h5tools_setstatus(EXIT_FAILURE);
         goto done;
     }
diff --git a/tools/src/h5repack/h5repack_opttable.c b/tools/src/h5repack/h5repack_opttable.c
index 4e6e0f4..2018527 100644
--- a/tools/src/h5repack/h5repack_opttable.c
+++ b/tools/src/h5repack/h5repack_opttable.c
@@ -104,7 +104,7 @@ aux_inctable(pack_opttbl_t *table, unsigned n_objs)
     int      ret_value = 0;
 
     table->size += n_objs;
-    table->objs = (pack_info_t *)HDrealloc(table->objs, table->size * sizeof(pack_info_t));
+    table->objs = (pack_info_t *)realloc(table->objs, table->size * sizeof(pack_info_t));
     if (table->objs == NULL) {
         H5TOOLS_INFO("not enough memory for options table");
         ret_value = -1;
@@ -132,14 +132,14 @@ options_table_init(pack_opttbl_t **tbl)
     pack_opttbl_t *table;
     int            ret_value = 0;
 
-    if (NULL == (table = (pack_opttbl_t *)HDmalloc(sizeof(pack_opttbl_t)))) {
+    if (NULL == (table = (pack_opttbl_t *)malloc(sizeof(pack_opttbl_t)))) {
         H5TOOLS_GOTO_ERROR((-1), "not enough memory for options table");
     }
 
     table->size   = 30;
     table->nelems = 0;
-    if (NULL == (table->objs = (pack_info_t *)HDmalloc(table->size * sizeof(pack_info_t)))) {
-        HDfree(table);
+    if (NULL == (table->objs = (pack_info_t *)malloc(table->size * sizeof(pack_info_t)))) {
+        free(table);
         H5TOOLS_GOTO_ERROR((-1), "not enough memory for options table");
     }
 
@@ -163,8 +163,8 @@ done:
 int
 options_table_free(pack_opttbl_t *table)
 {
-    HDfree(table->objs);
-    HDfree(table);
+    free(table->objs);
+    free(table);
     return 0;
 }
 
@@ -200,7 +200,7 @@ options_add_layout(obj_list_t *obj_list, unsigned n_objs, pack_info_t *pack, pac
                     /* already chunk info inserted for this one; exit */
                     if (table->objs[i].chunk.rank > 0) {
                         H5TOOLS_INFO("chunk information already inserted for <%s>\n", obj_list[j].obj);
-                        HDexit(EXIT_FAILURE);
+                        exit(EXIT_FAILURE);
                     }
                     /* insert the layout info */
                     else {
diff --git a/tools/src/h5repack/h5repack_parse.c b/tools/src/h5repack/h5repack_parse.c
index 9ffee0a..9ee4d07 100644
--- a/tools/src/h5repack/h5repack_parse.c
+++ b/tools/src/h5repack/h5repack_parse.c
@@ -52,7 +52,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
     unsigned    pixels_per_block;
 
     /* initialize compression  info */
-    HDmemset(filt, 0, sizeof(filter_info_t));
+    memset(filt, 0, sizeof(filter_info_t));
     *is_glb = 0;
 
     /* check for the end of object list and number of objects */
@@ -77,7 +77,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
     else
         *n_objs = n;
 
-    obj_list = (obj_list_t *)HDmalloc(n * sizeof(obj_list_t));
+    obj_list = (obj_list_t *)malloc(n * sizeof(obj_list_t));
     if (obj_list == NULL) {
         error_msg("could not allocate object list\n");
         return NULL;
@@ -95,7 +95,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                     sobj[k + 1] = '\0';
 
                 HDstrcpy(obj_list[n].obj, sobj);
-                HDmemset(sobj, 0, sizeof(sobj));
+                memset(sobj, 0, sizeof(sobj));
                 n++;
                 k = -1;
             }
@@ -103,9 +103,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
     /* nothing after : */
     if (end_obj + 1 == (int)len) {
         if (obj_list)
-            HDfree(obj_list);
+            free(obj_list);
         error_msg("input Error: Invalid compression type in <%s>\n", str);
-        HDexit(EXIT_FAILURE);
+        exit(EXIT_FAILURE);
     }
 
     /* get filter additional parameters */
@@ -134,9 +134,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                         c = str[u];
                         if (!HDisdigit(c) && l == -1) {
                             if (obj_list)
-                                HDfree(obj_list);
+                                free(obj_list);
                             error_msg("compression parameter not digit in <%s>\n", str);
-                            HDexit(EXIT_FAILURE);
+                            exit(EXIT_FAILURE);
                         }
                         if (l == -1)
                             stype[m] = c;
@@ -152,7 +152,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                                     filt->cd_values[j++] = H5_SZIP_EC_OPTION_MASK;
                                 else {
                                     error_msg("szip mask must be 'NN' or 'EC' \n");
-                                    HDexit(EXIT_FAILURE);
+                                    exit(EXIT_FAILURE);
                                 }
                             }
                         }
@@ -184,9 +184,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                         c = str[u];
                         if (!HDisdigit(c) && l == -1) {
                             if (obj_list)
-                                HDfree(obj_list);
+                                free(obj_list);
                             error_msg("compression parameter is not a digit in <%s>\n", str);
-                            HDexit(EXIT_FAILURE);
+                            exit(EXIT_FAILURE);
                         }
                         if (l == -1)
                             stype[m] = c;
@@ -202,7 +202,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                                     filt->cd_values[j++] = H5Z_SO_FLOAT_DSCALE;
                                 else {
                                     error_msg("scale type must be 'IN' or 'DS' \n");
-                                    HDexit(EXIT_FAILURE);
+                                    exit(EXIT_FAILURE);
                                 }
                             }
                         }
@@ -224,7 +224,7 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                         if (str[u] == ',') {
                             stype[q] = '\0'; /* end digit */
                             if (l == -1) {
-                                filt->filtn = HDatoi(stype);
+                                filt->filtn = atoi(stype);
                                 l           = 0;
                             }
                             else if (f == -1) {
@@ -244,15 +244,15 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                         c = str[u];
                         if (!HDisdigit(c) && l == -1) {
                             if (obj_list)
-                                HDfree(obj_list);
+                                free(obj_list);
                             error_msg("filter number parameter is not a digit in <%s>\n", str);
-                            HDexit(EXIT_FAILURE);
+                            exit(EXIT_FAILURE);
                         }
                         else if (!HDisdigit(c) && f == -1) {
                             if (obj_list)
-                                HDfree(obj_list);
+                                free(obj_list);
                             error_msg("filter flag parameter is not a digit in <%s>\n", str);
-                            HDexit(EXIT_FAILURE);
+                            exit(EXIT_FAILURE);
                         }
                         stype[q] = c;
                     } /* for u */
@@ -269,9 +269,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                         c = str[u];
                         if (!HDisdigit(c)) {
                             if (obj_list)
-                                HDfree(obj_list);
+                                free(obj_list);
                             error_msg("compression parameter is not a digit in <%s>\n", str);
-                            HDexit(EXIT_FAILURE);
+                            exit(EXIT_FAILURE);
                         }
                         stype[m] = c;
                     } /* u */
@@ -312,9 +312,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                 filt->cd_nelmts = 1;
                 if (no_param) { /*no more parameters, GZIP must have parameter */
                     if (obj_list)
-                        HDfree(obj_list);
+                        free(obj_list);
                     error_msg("missing compression parameter in <%s>\n", str);
-                    HDexit(EXIT_FAILURE);
+                    exit(EXIT_FAILURE);
                 }
             }
 
@@ -327,9 +327,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                 filt->cd_nelmts = 2;
                 if (no_param) { /*no more parameters, SZIP must have parameter */
                     if (obj_list)
-                        HDfree(obj_list);
+                        free(obj_list);
                     error_msg("missing compression parameter in <%s>\n", str);
-                    HDexit(EXIT_FAILURE);
+                    exit(EXIT_FAILURE);
                 }
             }
 
@@ -342,9 +342,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                 filt->cd_nelmts = 0;
                 if (m > 0) { /*shuffle does not have parameter */
                     if (obj_list)
-                        HDfree(obj_list);
+                        free(obj_list);
                     error_msg("extra parameter in SHUF <%s>\n", str);
-                    HDexit(EXIT_FAILURE);
+                    exit(EXIT_FAILURE);
                 }
             }
             /*-------------------------------------------------------------------------
@@ -356,9 +356,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                 filt->cd_nelmts = 0;
                 if (m > 0) { /*shuffle does not have parameter */
                     if (obj_list)
-                        HDfree(obj_list);
+                        free(obj_list);
                     error_msg("extra parameter in FLET <%s>\n", str);
-                    HDexit(EXIT_FAILURE);
+                    exit(EXIT_FAILURE);
                 }
             }
             /*-------------------------------------------------------------------------
@@ -370,9 +370,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                 filt->cd_nelmts = 0;
                 if (m > 0) { /*nbit does not have parameter */
                     if (obj_list)
-                        HDfree(obj_list);
+                        free(obj_list);
                     error_msg("extra parameter in NBIT <%s>\n", str);
-                    HDexit(EXIT_FAILURE);
+                    exit(EXIT_FAILURE);
                 }
             }
             /*-------------------------------------------------------------------------
@@ -384,9 +384,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                 filt->cd_nelmts = 2;
                 if (no_param) { /*no more parameters, SOFF must have parameter */
                     if (obj_list)
-                        HDfree(obj_list);
+                        free(obj_list);
                     error_msg("missing compression parameter in <%s>\n", str);
-                    HDexit(EXIT_FAILURE);
+                    exit(EXIT_FAILURE);
                 }
             }
             /*-------------------------------------------------------------------------
@@ -397,16 +397,16 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
                 /* parameters does not match count */
                 if (filt->cd_nelmts != j) {
                     if (obj_list)
-                        HDfree(obj_list);
+                        free(obj_list);
                     error_msg("incorrect number of compression parameters in <%s>\n", str);
-                    HDexit(EXIT_FAILURE);
+                    exit(EXIT_FAILURE);
                 }
             }
             else {
                 if (obj_list)
-                    HDfree(obj_list);
+                    free(obj_list);
                 error_msg("invalid filter type in <%s>\n", str);
-                HDexit(EXIT_FAILURE);
+                exit(EXIT_FAILURE);
             }
             break;
         }
@@ -425,9 +425,9 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
         case H5Z_FILTER_DEFLATE:
             if (filt->cd_values[0] > 9) {
                 if (obj_list)
-                    HDfree(obj_list);
+                    free(obj_list);
                 error_msg("invalid compression parameter in <%s>\n", str);
-                HDexit(EXIT_FAILURE);
+                exit(EXIT_FAILURE);
             }
             break;
             /*-------------------------------------------------------------------------
@@ -438,21 +438,21 @@ parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt, pack_opt_t
             pixels_per_block = filt->cd_values[0];
             if ((pixels_per_block % 2) == 1) {
                 if (obj_list)
-                    HDfree(obj_list);
+                    free(obj_list);
                 error_msg("pixels_per_block is not even in <%s>\n", str);
-                HDexit(EXIT_FAILURE);
+                exit(EXIT_FAILURE);
             }
             if (pixels_per_block > H5_SZIP_MAX_PIXELS_PER_BLOCK) {
                 if (obj_list)
-                    HDfree(obj_list);
+                    free(obj_list);
                 error_msg("pixels_per_block is too large in <%s>\n", str);
-                HDexit(EXIT_FAILURE);
+                exit(EXIT_FAILURE);
             }
             if ((HDstrcmp(smask, "NN") != 0) && (HDstrcmp(smask, "EC") != 0)) {
                 if (obj_list)
-                    HDfree(obj_list);
+                    free(obj_list);
                 error_msg("szip mask must be 'NN' or 'EC' \n");
-                HDexit(EXIT_FAILURE);
+                exit(EXIT_FAILURE);
             }
             break;
         default:
@@ -496,9 +496,9 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about
     char        sdim[10];
     char        slayout[10];
 
-    HDmemset(sdim, '\0', sizeof(sdim));
-    HDmemset(sobj, '\0', sizeof(sobj));
-    HDmemset(slayout, '\0', sizeof(slayout));
+    memset(sdim, '\0', sizeof(sdim));
+    memset(sobj, '\0', sizeof(sobj));
+    memset(slayout, '\0', sizeof(slayout));
 
     /* check for the end of object list and number of objects */
     for (i = 0, n = 0; i < len; i++) {
@@ -514,7 +514,7 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about
     }
 
     n++;
-    obj_list = (obj_list_t *)HDmalloc(n * sizeof(obj_list_t));
+    obj_list = (obj_list_t *)malloc(n * sizeof(obj_list_t));
     if (obj_list == NULL) {
         error_msg("could not allocate object list\n");
         return NULL;
@@ -532,7 +532,7 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about
                 else
                     sobj[k + 1] = '\0';
                 HDstrcpy(obj_list[n].obj, sobj);
-                HDmemset(sobj, 0, sizeof(sobj));
+                memset(sobj, 0, sizeof(sobj));
                 n++;
                 k = -1;
             }
@@ -541,9 +541,9 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about
     /* nothing after : */
     if (end_obj + 1 == (int)len) {
         if (obj_list)
-            HDfree(obj_list);
+            free(obj_list);
         error_msg("in parse layout, no characters after : in <%s>\n", str);
-        HDexit(EXIT_FAILURE);
+        exit(EXIT_FAILURE);
     }
 
     /* get layout info */
@@ -558,7 +558,7 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about
                 pack->layout = H5D_CHUNKED;
             else {
                 error_msg("in parse layout, not a valid layout in <%s>\n", str);
-                HDexit(EXIT_FAILURE);
+                exit(EXIT_FAILURE);
             }
         }
         else {
@@ -575,9 +575,9 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about
         k = 0;
         if (j > len) {
             if (obj_list)
-                HDfree(obj_list);
+                free(obj_list);
             error_msg("in parse layout,  <%s> Chunk dimensions missing\n", str);
-            HDexit(EXIT_FAILURE);
+            exit(EXIT_FAILURE);
         }
 
         for (i = j, c_index = 0; i < len; i++) {
@@ -587,9 +587,9 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about
 
             if (!HDisdigit(c) && c != 'x' && c != 'N' && c != 'O' && c != 'N' && c != 'E') {
                 if (obj_list)
-                    HDfree(obj_list);
+                    free(obj_list);
                 error_msg("in parse layout, <%s> Not a valid character in <%s>\n", sdim, str);
-                HDexit(EXIT_FAILURE);
+                exit(EXIT_FAILURE);
             }
 
             if (c == 'x' || i == len - 1) {
@@ -599,9 +599,9 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about
                     pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0);
                     if (pack->chunk.chunk_lengths[c_index] == 0) {
                         if (obj_list)
-                            HDfree(obj_list);
+                            free(obj_list);
                         error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str);
-                        HDexit(EXIT_FAILURE);
+                        exit(EXIT_FAILURE);
                     }
                     c_index++;
                 }
@@ -615,9 +615,9 @@ parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about
                         pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0);
                         if (pack->chunk.chunk_lengths[c_index] == 0) {
                             if (obj_list)
-                                HDfree(obj_list);
+                                free(obj_list);
                             error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str);
-                            HDexit(EXIT_FAILURE);
+                            exit(EXIT_FAILURE);
                         }
                         pack->chunk.rank = c_index + 1;
                     }
diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c
index 3c0be30..171b335 100644
--- a/tools/src/h5repack/h5repack_refs.c
+++ b/tools/src/h5repack/h5repack_refs.c
@@ -152,18 +152,18 @@ do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                          *-------------------------------------------------------------------------
                          */
                         if (nelmts) {
-                            buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
+                            buf = (hobj_ref_t *)malloc((unsigned)(nelmts * msize));
                             if (buf == NULL) {
-                                HDprintf("cannot read into memory\n");
-                                H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed");
+                                printf("cannot read into memory\n");
+                                H5TOOLS_GOTO_ERROR((-1), "malloc failed");
                             } /* end if */
                             if (H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
                                 H5TOOLS_GOTO_ERROR((-1), "H5Dread failed");
 
-                            refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize);
+                            refbuf = (hobj_ref_t *)calloc((unsigned)nelmts, msize);
                             if (refbuf == NULL) {
-                                HDprintf("cannot allocate memory\n");
-                                H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed");
+                                printf("cannot allocate memory\n");
+                                H5TOOLS_GOTO_ERROR((-1), "calloc failed");
                             } /* end if */
                             for (u = 0; u < nelmts; u++) {
                                 H5E_BEGIN_TRY
@@ -183,11 +183,11 @@ do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                         H5TOOLS_GOTO_ERROR((-1), "H5Rcreate failed");
                                     if (options->verbose > 0) {
                                         if (options->verbose == 2)
-                                            HDprintf(FORMAT_OBJ_NOTIME, "dset", travt->objs[i].name);
+                                            printf(FORMAT_OBJ_NOTIME, "dset", travt->objs[i].name);
                                         else
-                                            HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name);
-                                        HDprintf("object <%s> object reference created to <%s>\n",
-                                                 travt->objs[i].name, refname);
+                                            printf(FORMAT_OBJ, "dset", travt->objs[i].name);
+                                        printf("object <%s> object reference created to <%s>\n",
+                                               travt->objs[i].name, refname);
                                     }
                                 } /*refname*/
                                 if (H5Oclose(refobj_id) < 0)
@@ -207,9 +207,9 @@ do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                 H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed");
 
                         if (buf)
-                            HDfree(buf);
+                            free(buf);
                         if (refbuf)
-                            HDfree(refbuf);
+                            free(refbuf);
 
                         /*------------------------------------------------------
                          * copy attrs
@@ -234,10 +234,10 @@ do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                          *-------------------------------------------------------------------------
                          */
                         if (nelmts) {
-                            buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
+                            buf = (hdset_reg_ref_t *)malloc((unsigned)(nelmts * msize));
                             if (buf == NULL) {
-                                HDprintf("cannot read into memory\n");
-                                H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed");
+                                printf("cannot read into memory\n");
+                                H5TOOLS_GOTO_ERROR((-1), "malloc failed");
                             } /* end if */
                             if (H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
                                 H5TOOLS_GOTO_ERROR((-1), "H5Dread failed");
@@ -246,11 +246,11 @@ do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                              * create output
                              *-------------------------------------------------------------------------
                              */
-                            refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t),
-                                                                 (size_t)nelmts); /*init to zero */
+                            refbuf = (hdset_reg_ref_t *)calloc(sizeof(hdset_reg_ref_t),
+                                                               (size_t)nelmts); /*init to zero */
                             if (refbuf == NULL) {
-                                HDprintf("cannot allocate memory\n");
-                                H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed");
+                                printf("cannot allocate memory\n");
+                                H5TOOLS_GOTO_ERROR((-1), "calloc failed");
                             } /* end if */
 
                             for (u = 0; u < nelmts; u++) {
@@ -279,9 +279,9 @@ do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                     if (H5Sclose(region_id) < 0)
                                         H5TOOLS_GOTO_ERROR((-1), "H5Sclose failed");
                                     if (options->verbose > 0) {
-                                        HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name);
-                                        HDprintf("object <%s> region reference created to <%s>\n",
-                                                 travt->objs[i].name, refname);
+                                        printf(FORMAT_OBJ, "dset", travt->objs[i].name);
+                                        printf("object <%s> region reference created to <%s>\n",
+                                               travt->objs[i].name, refname);
                                     }
                                 } /*refname*/
                                 if (H5Oclose(refobj_id) < 0)
@@ -301,9 +301,9 @@ do_copy_refobjs(hid_t fidin, hid_t fidout, trav_table_t *travt, pack_opt_t *opti
                                 H5TOOLS_GOTO_ERROR((-1), "H5Dwrite failed");
 
                         if (buf)
-                            HDfree(buf);
+                            free(buf);
                         if (refbuf)
-                            HDfree(refbuf);
+                            free(refbuf);
 
                         /*-----------------------------------------------------
                          * copy attrs
@@ -506,8 +506,8 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
             if (nmembers < 1)
                 H5TOOLS_GOTO_ERROR((-1), "H5Tget_nmembers failed");
 
-            ref_comp_index   = (unsigned *)HDmalloc((size_t)nmembers * sizeof(unsigned));
-            ref_comp_size    = (size_t *)HDmalloc((size_t)nmembers * sizeof(ref_comp_size));
+            ref_comp_index   = (unsigned *)malloc((size_t)nmembers * sizeof(unsigned));
+            ref_comp_size    = (size_t *)malloc((size_t)nmembers * sizeof(ref_comp_size));
             ref_comp_field_n = 0;
 
             for (i = 0; i < (unsigned)nmembers; i++) {
@@ -527,12 +527,12 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
              * statement below. */
             if (!ref_comp_field_n) {
                 if (ref_comp_index) {
-                    HDfree(ref_comp_index);
+                    free(ref_comp_index);
                     ref_comp_index = NULL;
                 }
 
                 if (ref_comp_size) {
-                    HDfree(ref_comp_size);
+                    free(ref_comp_size);
                     ref_comp_size = NULL;
                 }
             }
@@ -598,18 +598,18 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
         if (nelmts > 0) {
             /* handle object references */
             if ((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE == msize)) {
-                buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
+                buf = (hobj_ref_t *)malloc((unsigned)(nelmts * msize));
                 if (buf == NULL) {
-                    HDprintf("cannot read into memory\n");
-                    H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed");
+                    printf("cannot read into memory\n");
+                    H5TOOLS_GOTO_ERROR((-1), "malloc failed");
                 } /* end if */
                 if (H5Aread(attr_id, mtype_id, buf) < 0)
                     H5TOOLS_GOTO_ERROR((-1), "H5Aread failed");
 
-                refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize);
+                refbuf = (hobj_ref_t *)calloc((unsigned)nelmts, msize);
                 if (refbuf == NULL) {
-                    HDprintf("cannot allocate memory\n");
-                    H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed");
+                    printf("cannot allocate memory\n");
+                    H5TOOLS_GOTO_ERROR((-1), "calloc failed");
                 } /* end if */
 
                 for (i = 0; i < (unsigned)nelmts; i++)
@@ -619,11 +619,11 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
             } /* H5T_STD_REF_OBJ */
             /* handle region references */
             else if ((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) {
-                buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
+                buf = (hdset_reg_ref_t *)malloc((unsigned)(nelmts * msize));
 
                 if (buf == NULL) {
-                    HDprintf("cannot read into memory\n");
-                    H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed");
+                    printf("cannot read into memory\n");
+                    H5TOOLS_GOTO_ERROR((-1), "malloc failed");
                 } /* end if */
                 if (H5Aread(attr_id, mtype_id, buf) < 0)
                     H5TOOLS_GOTO_ERROR((-1), "H5Aread failed");
@@ -632,11 +632,10 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
                  * create output
                  *-------------------------------------------------------------------------
                  */
-                refbuf =
-                    (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
+                refbuf = (hdset_reg_ref_t *)calloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
                 if (refbuf == NULL) {
-                    HDprintf("cannot allocate memory\n");
-                    H5TOOLS_GOTO_ERROR((-1), "HDcalloc failed");
+                    printf("cannot allocate memory\n");
+                    H5TOOLS_GOTO_ERROR((-1), "calloc failed");
                 } /* end if */
 
                 for (i = 0; i < (unsigned)nelmts; i++)
@@ -647,12 +646,12 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
             else if (is_ref_vlen) {
                 /* handle VLEN of references */
 
-                buf    = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t)));
+                buf    = (hvl_t *)malloc((unsigned)(nelmts * sizeof(hvl_t)));
                 refbuf = buf; /* reuse the read buffer for write */
 
                 if (buf == NULL) {
-                    HDprintf("cannot read into memory\n");
-                    H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed");
+                    printf("cannot read into memory\n");
+                    H5TOOLS_GOTO_ERROR((-1), "malloc failed");
                 } /* end if */
 
                 if (H5Aread(attr_id, mtype_id, buf) < 0)
@@ -667,7 +666,7 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
                         for (j = 0; j < ((hvl_t *)buf)[i].len; j++) {
                             if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt) < 0)
                                 continue;
-                            HDmemcpy(&(ptr[j]), &ref_out, msize);
+                            memcpy(&(ptr[j]), &ref_out, msize);
                         }
                     } /* for (i=0; i<nelems; i++) */
                 }
@@ -681,7 +680,7 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
                             if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out,
                                                  travt) < 0)
                                 continue;
-                            HDmemcpy(&(ptr[j]), &ref_out, msize);
+                            memcpy(&(ptr[j]), &ref_out, msize);
                         }
                     } /* for (i=0; i<nelems; i++) */
                 }
@@ -689,12 +688,12 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
             else if (is_ref_comp) {
                 /* handle ref fields in a compound */
 
-                buf    = HDmalloc((unsigned)(nelmts * msize));
+                buf    = malloc((unsigned)(nelmts * msize));
                 refbuf = buf; /* reuse the read buffer for write */
 
                 if (buf == NULL) {
-                    HDprintf("cannot read into memory\n");
-                    H5TOOLS_GOTO_ERROR((-1), "HDmalloc failed");
+                    printf("cannot read into memory\n");
+                    H5TOOLS_GOTO_ERROR((-1), "malloc failed");
                 } /* end if */
 
                 if (H5Aread(attr_id, mtype_id, buf) < 0)
@@ -712,7 +711,7 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
                                                  travt) < 0) /* Extra (void *) cast to quiet "cast to create
                                                                 alignment" warning - 2019/07/05, QAK */
                                 continue;
-                            HDmemcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]);
+                            memcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]);
                         } /* if */
                         else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
                             size_t idx = i * msize + H5Tget_member_offset(mtype_id, ref_comp_index[j]);
@@ -722,7 +721,7 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
                                                  (hdset_reg_ref_t *)(((char *)buf) + idx), fidout, &ref_out,
                                                  travt) < 0)
                                 continue;
-                            HDmemcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]);
+                            memcpy(((char *)buf) + idx, &ref_out, ref_comp_size[j]);
                         } /* else if */
                     }     /* j */
                 }         /* i */
@@ -739,22 +738,22 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
             refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
 
         if (buf) {
-            HDfree(buf);
+            free(buf);
             buf = NULL;
         }
 
         if (refbuf) {
-            HDfree(refbuf);
+            free(refbuf);
             refbuf = NULL;
         }
 
         if (ref_comp_index) {
-            HDfree(ref_comp_index);
+            free(ref_comp_index);
             ref_comp_index = NULL;
         }
 
         if (ref_comp_size) {
-            HDfree(ref_comp_size);
+            free(ref_comp_size);
             ref_comp_size = NULL;
         }
 
@@ -777,15 +776,15 @@ copy_refs_attr(hid_t loc_in, hid_t loc_out, trav_table_t *travt, hid_t fidout) /
 
 done:
     if (refbuf)
-        HDfree(refbuf);
+        free(refbuf);
     if (buf)
-        HDfree(buf);
+        free(buf);
 
     if (ref_comp_index)
-        HDfree(ref_comp_index);
+        free(ref_comp_index);
 
     if (ref_comp_size)
-        HDfree(ref_comp_size);
+        free(ref_comp_size);
 
     H5E_BEGIN_TRY
     {