Sync branch with develop (#1616)feature/parallel_h5repack

Sync branch with develop

26 files changed, 223 insertions, 202 deletions

diff --git a/tools/src/h5copy/h5copy.c b/tools/src/h5copy/h5copy.c
index 4e9a25e..eacd05b 100644
--- a/tools/src/h5copy/h5copy.c
+++ b/tools/src/h5copy/h5copy.c
@@ -19,7 +19,7 @@
 #define PROGRAMNAME "h5copy"
 
 /* command-line options: short and long-named parameters */
-static const char *           s_opts    = "d:f:hi:o:ps:vVE";
+static const char *           s_opts    = "d:f:hi:o:ps:vVE*";
 static struct h5_long_options l_opts[]  = {{"destination", require_arg, 'd'},
                                           {"flag", require_arg, 'f'},
                                           {"help", no_arg, 'h'},
@@ -29,7 +29,7 @@ static struct h5_long_options l_opts[]  = {{"destination", require_arg, 'd'},
                                           {"source", require_arg, 's'},
                                           {"verbose", no_arg, 'v'},
                                           {"version", no_arg, 'V'},
-                                          {"enable-error-stack", no_arg, 'E'},
+                                          {"enable-error-stack", optional_arg, 'E'},
                                           {NULL, 0, '\0'}};
 char *                        fname_src = NULL;
 char *                        fname_dst = NULL;
@@ -93,15 +93,17 @@ usage(void)
     PRINTVALSTREAM(rawoutstream, "      -o, --output       output file name\n");
     PRINTVALSTREAM(rawoutstream, "      -s, --source       source object name\n");
     PRINTVALSTREAM(rawoutstream, "      -d, --destination  destination object name\n");
+    PRINTVALSTREAM(rawoutstream, "   ERROR\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "     --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "                          Optional value 2 also prints file open errors.\n");
     PRINTVALSTREAM(rawoutstream, "   OPTIONS\n");
     PRINTVALSTREAM(rawoutstream, "      -h, --help         Print a usage message and exit\n");
     PRINTVALSTREAM(rawoutstream,
                    "      -p, --parents      No error if existing, make parent groups as needed\n");
     PRINTVALSTREAM(rawoutstream, "      -v, --verbose      Print information about OBJECTS and OPTIONS\n");
     PRINTVALSTREAM(rawoutstream, "      -V, --version      Print version number and exit\n");
-    PRINTVALSTREAM(rawoutstream, "      --enable-error-stack\n");
-    PRINTVALSTREAM(rawoutstream,
-                   "                  Prints messages from the HDF5 error stack as they occur.\n");
     PRINTVALSTREAM(rawoutstream, "      -f, --flag         Flag type\n\n");
     PRINTVALSTREAM(rawoutstream, "      Flag type is one of the following strings:\n\n");
     PRINTVALSTREAM(rawoutstream, "      shallow     Copy only immediate members for groups\n\n");
@@ -212,7 +214,7 @@ parse_flag(const char *s_flag, unsigned *flag)
  */
 
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     hid_t              fid_src = H5I_INVALID_HID;
     hid_t              fid_dst = H5I_INVALID_HID;
@@ -242,7 +244,7 @@ main(int argc, const char *argv[])
     } /* end if */
 
     /* parse command line options */
-    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, (const char *const *)argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'd':
                 oname_dst = HDstrdup(H5_optarg);
@@ -288,7 +290,10 @@ main(int argc, const char *argv[])
                 break;
 
             case 'E':
-                enable_error_stack = 1;
+                if (H5_optarg != NULL)
+                    enable_error_stack = HDatoi(H5_optarg);
+                else
+                    enable_error_stack = 1;
                 break;
 
             default:
diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c
index 9dcd91b..98ac8f7 100644
--- a/tools/src/h5diff/h5diff_common.c
+++ b/tools/src/h5diff/h5diff_common.c
@@ -25,7 +25,7 @@ static int check_d_input(const char *);
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *           s_opts   = "hVrv*qn:d:p:NcelxE:A:S";
+static const char *           s_opts   = "hVrv*qn:d:p:NcelxE:A:S*";
 static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
                                           {"version", no_arg, 'V'},
                                           {"report", no_arg, 'r'},
@@ -41,7 +41,7 @@ static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
                                           {"no-dangling-links", no_arg, 'x'},
                                           {"exclude-path", require_arg, 'E'},
                                           {"exclude-attribute", require_arg, 'A'},
-                                          {"enable-error-stack", no_arg, 'S'},
+                                          {"enable-error-stack", optional_arg, 'S'},
                                           {"vol-value-1", require_arg, '1'},
                                           {"vol-name-1", require_arg, '2'},
                                           {"vol-info-1", require_arg, '3'},
@@ -217,7 +217,7 @@ parse_subset_params(const char *dset)
  */
 
 void
-parse_command_line(int argc, const char *argv[], const char **fname1, const char **fname2,
+parse_command_line(int argc, const char *const *argv, const char **fname1, const char **fname2,
                    const char **objname1, const char **objname2, diff_opt_t *opts)
 {
     int                       i;
@@ -311,7 +311,10 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
                 break;
 
             case 'S':
-                enable_error_stack = 1;
+                if (H5_optarg != NULL)
+                    enable_error_stack = HDatoi(H5_optarg);
+                else
+                    enable_error_stack = 1;
                 break;
 
             case 'E':
@@ -705,6 +708,10 @@ usage(void)
     PRINTVALSTREAM(rawoutstream, "  [obj1]            Name of an HDF5 object, in absolute path\n");
     PRINTVALSTREAM(rawoutstream, "  [obj2]            Name of an HDF5 object, in absolute path\n");
     PRINTVALSTREAM(rawoutstream, "\n");
+    PRINTVALSTREAM(rawoutstream, "  ERROR\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "   --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n");
+    PRINTVALSTREAM(rawoutstream, "                        Optional value 2 also prints file open errors.\n");
     PRINTVALSTREAM(rawoutstream, "  OPTIONS\n");
     PRINTVALSTREAM(rawoutstream, "   -h, --help\n");
     PRINTVALSTREAM(rawoutstream, "         Print a usage message and exit.\n");
@@ -727,9 +734,6 @@ usage(void)
     PRINTVALSTREAM(rawoutstream, "          3 : All level 2 information plus file names.\n");
     PRINTVALSTREAM(rawoutstream, "   -q, --quiet\n");
     PRINTVALSTREAM(rawoutstream, "         Quiet mode. Do not produce output.\n");
-    PRINTVALSTREAM(rawoutstream, "   --enable-error-stack\n");
-    PRINTVALSTREAM(rawoutstream,
-                   "                   Prints messages from the HDF5 error stack as they occur.\n");
     PRINTVALSTREAM(rawoutstream,
                    "   --vol-value-1           Value (ID) of the VOL connector to use for opening the\n");
     PRINTVALSTREAM(rawoutstream, "                           first HDF5 file specified\n");
diff --git a/tools/src/h5diff/h5diff_common.h b/tools/src/h5diff/h5diff_common.h
index 83f4255..35e5dfb 100644
--- a/tools/src/h5diff/h5diff_common.h
+++ b/tools/src/h5diff/h5diff_common.h
@@ -23,7 +23,7 @@ extern "C" {
 #endif
 
 void usage(void);
-void parse_command_line(int argc, const char *argv[], const char **fname1, const char **fname2,
+void parse_command_line(int argc, const char *const *argv, const char **fname1, const char **fname2,
                         const char **objname1, const char **objname2, diff_opt_t *opts);
 void h5diff_exit(int status);
 void print_info(diff_opt_t *opts);
diff --git a/tools/src/h5diff/h5diff_main.c b/tools/src/h5diff/h5diff_main.c
index 37c215b..2a43b56 100644
--- a/tools/src/h5diff/h5diff_main.c
+++ b/tools/src/h5diff/h5diff_main.c
@@ -65,7 +65,7 @@
  */
 
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     int         ret;
     int         i;
@@ -86,7 +86,7 @@ main(int argc, const char *argv[])
      * process the command-line
      *-------------------------------------------------------------------------
      */
-    parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &opts);
+    parse_command_line(argc, (const char *const *)argv, &fname1, &fname2, &objname1, &objname2, &opts);
 
     /* enable error reporting if command line option */
     h5tools_error_report();
diff --git a/tools/src/h5diff/ph5diff_main.c b/tools/src/h5diff/ph5diff_main.c
index af6a29a..e93c1cd 100644
--- a/tools/src/h5diff/ph5diff_main.c
+++ b/tools/src/h5diff/ph5diff_main.c
@@ -46,7 +46,7 @@
  */
 
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     const char *fname1   = NULL;
     const char *fname2   = NULL;
diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c
index a57b0e3..d82ea94 100644
--- a/tools/src/h5dump/h5dump.c
+++ b/tools/src/h5dump/h5dump.c
@@ -165,6 +165,12 @@ usage(const char *prog)
     PRINTVALSTREAM(rawoutstream, "  OPTIONS\n");
     PRINTVALSTREAM(rawoutstream, "     -h,   --help         Print a usage message and exit\n");
     PRINTVALSTREAM(rawoutstream, "     -V,   --version      Print version number and exit\n");
+    PRINTVALSTREAM(rawoutstream, "--------------- Error Options ---------------\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "     --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "                          Optional value 2 also prints file open errors.\n");
+    PRINTVALSTREAM(rawoutstream, "                          Default setting disables any error reporting.\n");
     PRINTVALSTREAM(rawoutstream, "--------------- File Options ---------------\n");
     PRINTVALSTREAM(rawoutstream, "     -n,   --contents     Print a list of the file contents and exit\n");
     PRINTVALSTREAM(rawoutstream, "                          Optional value 1 also prints attributes.\n");
@@ -254,10 +260,6 @@ usage(const char *prog)
     PRINTVALSTREAM(rawoutstream, "     -q Q, --sort_by=Q    Sort groups and attributes by index Q\n");
     PRINTVALSTREAM(rawoutstream, "     -z Z, --sort_order=Z Sort groups and attributes by order Z\n");
     PRINTVALSTREAM(rawoutstream,
-                   "     --enable-error-stack Prints messages from the HDF5 error stack as they occur.\n");
-    PRINTVALSTREAM(rawoutstream,
-                   "                          Optional value 2 also prints file open errors.\n");
-    PRINTVALSTREAM(rawoutstream,
                    "     --no-compact-subset  Disable compact form of subsetting and allow the use\n");
     PRINTVALSTREAM(rawoutstream, "                          of \"[\" in dataset names.\n");
     PRINTVALSTREAM(rawoutstream,
@@ -828,7 +830,7 @@ free_handler(struct handler_t *hand, int len)
  *-------------------------------------------------------------------------
  */
 static struct handler_t *
-parse_command_line(int argc, const char *argv[])
+parse_command_line(int argc, const char *const *argv)
 {
     struct handler_t *hand      = NULL;
     struct handler_t *last_dset = NULL;
@@ -1329,7 +1331,7 @@ error:
  *-------------------------------------------------------------------------
  */
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     hid_t             fid     = H5I_INVALID_HID;
     hid_t             gid     = H5I_INVALID_HID;
@@ -1349,7 +1351,7 @@ main(int argc, const char *argv[])
     /* Initialize h5tools lib */
     h5tools_init();
 
-    if ((hand = parse_command_line(argc, argv)) == NULL) {
+    if ((hand = parse_command_line(argc, (const char *const *)argv)) == NULL) {
         goto done;
     }
 
diff --git a/tools/src/h5dump/h5dump_ddl.c b/tools/src/h5dump/h5dump_ddl.c
index 8002ec2..b0bce0c 100644
--- a/tools/src/h5dump/h5dump_ddl.c
+++ b/tools/src/h5dump/h5dump_ddl.c
@@ -838,7 +838,7 @@ dump_group(hid_t gid, const char *name)
                 type = H5Dget_type(dset);
 
                 H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str);
-                HDsprintf(type_name, "#%s", obj_tok_str);
+                HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str);
                 H5free_memory(obj_tok_str);
 
                 dump_function_table->dump_named_datatype_function(type, type_name);
@@ -1318,7 +1318,7 @@ attr_search(hid_t oid, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *a
     j = (int)HDstrlen(op_name) - 1;
     /* find the last / */
     while (j >= 0) {
-        if (op_name[j] == '/' && (j == 0 || (j > 0 && op_name[j - 1] != '\\')))
+        if (op_name[j] == '/' && (j == 0 || (op_name[j - 1] != '\\')))
             break;
         j--;
     }
@@ -1541,7 +1541,7 @@ handle_attributes(hid_t fid, const char *attr, void H5_ATTR_UNUSED *data, int H5
 
     /* find the last / */
     while (j >= 0) {
-        if (attr[j] == '/' && (j == 0 || (j > 0 && attr[j - 1] != '\\')))
+        if (attr[j] == '/' && (j == 0 || (attr[j - 1] != '\\')))
             break;
         j--;
     }
@@ -1970,7 +1970,7 @@ handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED *data, int pe,
 
                 /* unnamed datatype */
                 H5Otoken_to_str(fid, &type_table->objs[idx].obj_token, &obj_tok_str);
-                HDsprintf(name, "/#%s", obj_tok_str);
+                HDsnprintf(name, sizeof(name), "/#%s", obj_tok_str);
                 H5free_memory(obj_tok_str);
 
                 if (!HDstrcmp(name, real_name))
diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c
index 8fec49c..827daf3 100644
--- a/tools/src/h5dump/h5dump_xml.c
+++ b/tools/src/h5dump/h5dump_xml.c
@@ -591,6 +591,8 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
     if (outlen < 22)
         return 1;
 
+    H5_CHECK_OVERFLOW(outlen, int, size_t);
+
     lookup_ret = ref_path_table_lookup(str, &obj_token);
     if (lookup_ret < 0) {
         if (HDstrlen(str) == 0) {
@@ -600,7 +602,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
                     ref_path_table_gen_fake(str, &obj_token);
 
                     H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str);
-                    HDsprintf(outstr, "xid_%s", obj_tok_str);
+                    HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str);
                     H5free_memory(obj_tok_str);
 
                     return 0;
@@ -615,7 +617,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
                 ref_path_table_gen_fake(str, &obj_token);
 
                 H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str);
-                HDsprintf(outstr, "xid_%s", obj_tok_str);
+                HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str);
                 H5free_memory(obj_tok_str);
 
                 return 0;
@@ -627,7 +629,7 @@ xml_name_to_XID(hid_t loc_id, const char *str, char *outstr, int outlen, int gen
     }
 
     H5Otoken_to_str(loc_id, &obj_token, &obj_tok_str);
-    HDsprintf(outstr, "xid_%s", obj_tok_str);
+    HDsnprintf(outstr, (size_t)outlen, "xid_%s", obj_tok_str);
     H5free_memory(obj_tok_str);
 
     return 0;
@@ -1777,8 +1779,7 @@ xml_dump_dataspace(hid_t space)
                     /* Render the element */
                     h5tools_str_reset(&buffer);
                     h5tools_str_append(&buffer,
-                                       "<%sDimension  DimSize=\"%" H5_PRINTF_LL_WIDTH
-                                       "u\" MaxDimSize=\"UNLIMITED\"/>",
+                                       "<%sDimension  DimSize=\"%" PRIuHSIZE "\" MaxDimSize=\"UNLIMITED\"/>",
                                        xmlnsprefix, size[i]);
                     h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos,
                                            (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
@@ -1788,10 +1789,9 @@ xml_dump_dataspace(hid_t space)
 
                     /* Render the element */
                     h5tools_str_reset(&buffer);
-                    h5tools_str_append(&buffer,
-                                       "<%sDimension  DimSize=\"%" H5_PRINTF_LL_WIDTH
-                                       "u\" MaxDimSize=\"%" H5_PRINTF_LL_WIDTH "u\"/>",
-                                       xmlnsprefix, size[i], size[i]);
+                    h5tools_str_append(
+                        &buffer, "<%sDimension  DimSize=\"%" PRIuHSIZE "\" MaxDimSize=\"%" PRIuHSIZE "\"/>",
+                        xmlnsprefix, size[i], size[i]);
                     h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos,
                                            (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
                 }
@@ -1800,10 +1800,9 @@ xml_dump_dataspace(hid_t space)
 
                     /* Render the element */
                     h5tools_str_reset(&buffer);
-                    h5tools_str_append(&buffer,
-                                       "<%sDimension  DimSize=\"%" H5_PRINTF_LL_WIDTH
-                                       "u\" MaxDimSize=\"%" H5_PRINTF_LL_WIDTH "u\"/>",
-                                       xmlnsprefix, size[i], maxsize[i]);
+                    h5tools_str_append(
+                        &buffer, "<%sDimension  DimSize=\"%" PRIuHSIZE "\" MaxDimSize=\"%" PRIuHSIZE "\"/>",
+                        xmlnsprefix, size[i], maxsize[i]);
                     h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos,
                                            (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
                 }
@@ -2802,7 +2801,7 @@ xml_dump_group(hid_t gid, const char *name)
                             type = H5Dget_type(dset);
 
                             H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str);
-                            HDsprintf(type_name, "#%s", obj_tok_str);
+                            HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str);
                             H5free_memory(obj_tok_str);
 
                             dump_function_table->dump_named_datatype_function(type, type_name);
@@ -2895,7 +2894,7 @@ xml_dump_group(hid_t gid, const char *name)
                     type = H5Dget_type(dset);
 
                     H5Otoken_to_str(dset, &type_table->objs[u].obj_token, &obj_tok_str);
-                    HDsprintf(type_name, "#%s", obj_tok_str);
+                    HDsnprintf(type_name, sizeof(type_name), "#%s", obj_tok_str);
                     H5free_memory(obj_tok_str);
 
                     dump_function_table->dump_named_datatype_function(type, type_name);
@@ -3598,7 +3597,10 @@ xml_dump_fill_value(hid_t dcpl, hid_t type)
                 h5tools_str_reset(&buffer);
                 h5tools_str_append(&buffer, "\"");
                 for (i = 0; i < sz; i++) {
-                    h5tools_str_append(&buffer, "%x ", *(unsigned int *)buf + (i * sizeof(unsigned int)));
+                    unsigned long val = *(unsigned int *)buf + (i * sizeof(unsigned int));
+
+                    H5_CHECK_OVERFLOW(val, unsigned long, unsigned);
+                    h5tools_str_append(&buffer, "%x ", (unsigned)val);
                 }
                 h5tools_str_append(&buffer, "\"");
                 h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos,
@@ -3892,8 +3894,8 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED *ss
 
                 /* Render the element */
                 h5tools_str_reset(&buffer);
-                h5tools_str_append(&buffer, "<%sChunkDimension DimSize=\"%" H5_PRINTF_LL_WIDTH "u\" />",
-                                   xmlnsprefix, chsize[i]);
+                h5tools_str_append(&buffer, "<%sChunkDimension DimSize=\"%" PRIuHSIZE "\" />", xmlnsprefix,
+                                   chsize[i]);
                 h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos,
                                        (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
             }
@@ -4524,12 +4526,16 @@ xml_print_enum(hid_t type)
                 h5tools_str_append(&buffer, "%02x", value[i * dst_size + j]);
         }
         else if (H5T_SGN_NONE == H5Tget_sign(native)) {
-            h5tools_str_append(&buffer, "%" H5_PRINTF_LL_WIDTH "u",
-                               *((unsigned long long *)((void *)(value + i * dst_size))));
+            unsigned long long copy;
+
+            HDmemcpy(&copy, value + i * dst_size, sizeof(copy));
+            h5tools_str_append(&buffer, "%llu", copy);
         }
         else {
-            h5tools_str_append(&buffer, "%" H5_PRINTF_LL_WIDTH "d",
-                               *((long long *)((void *)(value + i * dst_size))));
+            long long copy;
+
+            HDmemcpy(&copy, value + i * dst_size, sizeof(copy));
+            h5tools_str_append(&buffer, "%lld", copy);
         }
         h5tools_render_element(rawoutstream, outputformat, &ctx, &buffer, &curr_pos,
                                (size_t)outputformat->line_ncols, (hsize_t)0, (hsize_t)0);
diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c
index ddf129c..50d0f5d 100644
--- a/tools/src/h5format_convert/h5format_convert.c
+++ b/tools/src/h5format_convert/h5format_convert.c
@@ -94,7 +94,7 @@ usage(const char *prog)
  *-------------------------------------------------------------------------
  */
 static int
-parse_command_line(int argc, const char **argv)
+parse_command_line(int argc, const char *const *argv)
 {
     int opt;
 
@@ -127,7 +127,7 @@ parse_command_line(int argc, const char **argv)
                     dname_g = HDstrdup(H5_optarg);
                 if (dname_g == NULL) {
                     h5tools_setstatus(EXIT_FAILURE);
-                    error_msg("No dataset name\n", H5_optarg);
+                    error_msg("No dataset name `%s`\n", H5_optarg);
                     usage(h5tools_getprogname());
                     goto error;
                 }
@@ -383,7 +383,7 @@ error:
  *-------------------------------------------------------------------------
  */
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     hid_t fid = H5I_INVALID_HID;
 
@@ -394,7 +394,7 @@ main(int argc, const char *argv[])
     h5tools_init();
 
     /* Parse command line options */
-    if (parse_command_line(argc, argv) < 0)
+    if (parse_command_line(argc, (const char *const *)argv) < 0)
         goto done;
     else if (verbose_g)
         HDfprintf(stdout, "Process command line options\n");
diff --git a/tools/src/h5import/h5import.c b/tools/src/h5import/h5import.c
index 31fa7cf..317db81 100644
--- a/tools/src/h5import/h5import.c
+++ b/tools/src/h5import/h5import.c
@@ -3784,7 +3784,7 @@ setDefaultValues(struct Input *in, int count)
     in->path.count     = 1;
 
     HDstrcpy(temp, "dataset");
-    HDsprintf(num, "%d", count);
+    HDsnprintf(num, sizeof(num), "%d", count);
     HDstrcat(temp, num);
     HDstrcpy(in->path.group[0], temp);
 
diff --git a/tools/src/h5jam/h5jam.c b/tools/src/h5jam/h5jam.c
index 07140b5..45978bb 100644
--- a/tools/src/h5jam/h5jam.c
+++ b/tools/src/h5jam/h5jam.c
@@ -22,7 +22,7 @@
 herr_t  write_pad(int ofile, hsize_t old_where, hsize_t *new_where);
 hsize_t compute_user_block_size(hsize_t);
 hsize_t copy_some_to_file(int, int, hsize_t, hsize_t, ssize_t);
-void    parse_command_line(int, const char *[]);
+void    parse_command_line(int, const char *const *);
 
 int   do_clobber  = FALSE;
 char *output_file = NULL;
@@ -104,7 +104,7 @@ leave(int ret)
  */
 
 void
-parse_command_line(int argc, const char *argv[])
+parse_command_line(int argc, const char *const *argv)
 {
     int opt = FALSE;
 
@@ -149,7 +149,7 @@ parse_command_line(int argc, const char *argv[])
  *-------------------------------------------------------------------------
  */
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     int       ufid  = -1;
     int       h5fid = -1;
@@ -174,7 +174,7 @@ main(int argc, const char *argv[])
     /* Initialize h5tools lib */
     h5tools_init();
 
-    parse_command_line(argc, argv);
+    parse_command_line(argc, (const char *const *)argv);
 
     /* enable error reporting if command line option */
     h5tools_error_report();
diff --git a/tools/src/h5jam/h5unjam.c b/tools/src/h5jam/h5unjam.c
index fa23b06..8ff354e 100644
--- a/tools/src/h5jam/h5unjam.c
+++ b/tools/src/h5jam/h5unjam.c
@@ -92,7 +92,7 @@ usage(const char *prog)
  *-------------------------------------------------------------------------
  */
 static int
-parse_command_line(int argc, const char *argv[])
+parse_command_line(int argc, const char *const *argv)
 {
     int opt = FALSE;
 
@@ -172,7 +172,7 @@ leave(int ret)
  *-------------------------------------------------------------------------
  */
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     hid_t     ifile = H5I_INVALID_HID;
     hid_t     plist = H5I_INVALID_HID;
@@ -189,7 +189,7 @@ main(int argc, const char *argv[])
     /* Initialize h5tools lib  */
     h5tools_init();
 
-    if (EXIT_FAILURE == parse_command_line(argc, argv))
+    if (EXIT_FAILURE == parse_command_line(argc, (const char *const *)argv))
         goto done;
 
     /* enable error reporting if command line option */
diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c
index 17abf43..c30c08f 100644
--- a/tools/src/h5ls/h5ls.c
+++ b/tools/src/h5ls/h5ls.c
@@ -78,9 +78,9 @@ static h5tool_format_t ls_dataformat = {
     ",",  /*elmt_suf1 */
     " ",  /*elmt_suf2 */
 
-    HSIZE_T_FORMAT, /*idx_n_fmt */
-    ",",            /*idx_sep */
-    "(%s)",         /*idx_fmt */
+    "%" PRIuHSIZE, /*idx_n_fmt */
+    ",",           /*idx_sep */
+    "(%s)",        /*idx_fmt */
 
     65535,
     /*line_ncols */ /*standard default columns */
@@ -942,8 +942,7 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind)
 
         /* Print members */
         for (i = 0; i < (unsigned)nmembs; i++) {
-            unsigned char *copy;   /* a pointer to value array */
-            int            nchars; /* number of output characters */
+            int nchars; /* number of output characters */
 
             h5tools_str_append(buffer, "\n%*s", ind + 4, "");
             nchars = print_string(buffer, name[i], TRUE);
@@ -957,16 +956,16 @@ print_enum_type(h5tools_str_t *buffer, hid_t type, int ind)
                     h5tools_str_append(buffer, "%02x", value[i * dst_size + j]);
             }
             else if (H5T_SGN_NONE == H5Tget_sign(native)) {
-                /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size"
-                 *strangely, unless use another pointer "copy".*/
-                copy = value + i * dst_size;
-                h5tools_str_append(buffer, HSIZE_T_FORMAT, *((unsigned long long *)((void *)copy)));
+                unsigned long long copy;
+
+                HDmemcpy(&copy, value + i * dst_size, sizeof(copy));
+                h5tools_str_append(buffer, "%llu", copy);
             }
             else {
-                /*On SGI Altix(cobalt), wrong values were printed out with "value+i*dst_size"
-                 *strangely, unless use another pointer "copy".*/
-                copy = value + i * dst_size;
-                h5tools_str_append(buffer, "%lld", *((long long *)((void *)copy)));
+                long long copy;
+
+                HDmemcpy(&copy, value + i * dst_size, sizeof(copy));
+                h5tools_str_append(buffer, "%lld", copy);
             }
         }
 
@@ -1185,13 +1184,13 @@ print_array_type(h5tools_str_t *buffer, hid_t type, int ind)
 
         /* Print dimensions */
         for (i = 0; i < ndims; i++)
-            h5tools_str_append(buffer, "%s" HSIZE_T_FORMAT, i ? "," : "[", dims[i]);
+            h5tools_str_append(buffer, "%s%" PRIuHSIZE, i ? "," : "[", dims[i]);
         h5tools_str_append(buffer, "]");
 
         HDfree(dims);
     }
     else
-        h5tools_str_append(buffer, " [SCALAR]\n", rawoutstream);
+        h5tools_str_append(buffer, " [SCALAR]\n");
 
     /* Print parent type */
     h5tools_str_append(buffer, " ");
@@ -1701,7 +1700,7 @@ list_attr(hid_t obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ain
                 /* simple dataspace */
                 h5tools_str_append(&buffer, " {");
                 for (i = 0; i < ndims; i++) {
-                    h5tools_str_append(&buffer, "%s" HSIZE_T_FORMAT, i ? ", " : "", size[i]);
+                    h5tools_str_append(&buffer, "%s%" PRIuHSIZE, i ? ", " : "", size[i]);
                     nelmts *= size[i];
                 }
                 h5tools_str_append(&buffer, "}\n");
@@ -1789,12 +1788,12 @@ dataset_list1(hid_t dset)
     ndims      = H5Sget_simple_extent_dims(space, cur_size, max_size);
     h5tools_str_append(&buffer, " {");
     for (i = 0; i < ndims; i++) {
-        h5tools_str_append(&buffer, "%s" HSIZE_T_FORMAT, i ? ", " : "", cur_size[i]);
+        h5tools_str_append(&buffer, "%s%" PRIuHSIZE, i ? ", " : "", cur_size[i]);
         if (max_size[i] == H5S_UNLIMITED) {
             h5tools_str_append(&buffer, "/%s", "Inf");
         }
         else if (max_size[i] != cur_size[i] || verbose_g > 0) {
-            h5tools_str_append(&buffer, "/" HSIZE_T_FORMAT, max_size[i]);
+            h5tools_str_append(&buffer, "/%" PRIuHSIZE, max_size[i]);
         }
     }
     if (space_type == H5S_SCALAR)
@@ -1868,10 +1867,10 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name)
                 h5tools_str_append(&buffer, "    %-10s {", "Chunks:");
                 total = H5Tget_size(type);
                 for (i = 0; i < ndims; i++) {
-                    h5tools_str_append(&buffer, "%s" HSIZE_T_FORMAT, i ? ", " : "", chsize[i]);
+                    h5tools_str_append(&buffer, "%s%" PRIuHSIZE, i ? ", " : "", chsize[i]);
                     total *= chsize[i];
                 }
-                h5tools_str_append(&buffer, "} " HSIZE_T_FORMAT " bytes\n", total);
+                h5tools_str_append(&buffer, "} %" PRIuHSIZE " bytes\n", total);
             } break;
             case H5D_COMPACT:
                 break;
@@ -1897,15 +1896,13 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name)
                         if (H5Pget_external(dcpl, (unsigned)i, sizeof(f_name), f_name, &f_offset, &f_size) <
                             0) {
                             h5tools_str_append(
-                                &buffer,
-                                "        #%03d %10" H5_PRINTF_LL_WIDTH "u %10s %10s ***ERROR*** %s\n", i,
+                                &buffer, "        #%03d %10" PRIuHSIZE " %10s %10s ***ERROR*** %s\n", i,
                                 total, "", "", i + 1 < nf ? "Following addresses are incorrect" : "");
                         }
                         else if (H5S_UNLIMITED == f_size) {
                             h5tools_str_append(&buffer,
-                                               "        #%03d %10" H5_PRINTF_LL_WIDTH
-                                               "u %10" H5_PRINTF_LL_WIDTH "u %10s ",
-                                               i, total, (hsize_t)f_offset, "INF");
+                                               "        #%03d %10" PRIuHSIZE " %10" PRIuHSIZE " %10s ", i,
+                                               total, (hsize_t)f_offset, "INF");
                             print_string(&buffer, f_name, TRUE);
                         }
                         else {
@@ -1985,8 +1982,7 @@ dataset_list2(hid_t dset, const char H5_ATTR_UNUSED *name)
             case H5T_ARRAY:
             case H5T_NCLASSES:
             default:
-                h5tools_str_append(&buffer,
-                                   HSIZE_T_FORMAT " logical byte%s, " HSIZE_T_FORMAT " allocated byte%s",
+                h5tools_str_append(&buffer, "%" PRIuHSIZE " logical byte%s, %" PRIuHSIZE " allocated byte%s",
                                    total, 1 == total ? "" : "s", used, 1 == used ? "" : "s");
                 if (used > 0) {
                     utilization = ((double)total * 100.0) / (double)used;
@@ -2303,7 +2299,7 @@ list_lnk(const char *name, const H5L_info2_t *linfo, void *_iter)
                 iter->symlink_list->dangle_link = TRUE;
 
             h5tools_str_append(&buffer, "Soft Link {");
-            h5tools_str_append(&buffer, buf);
+            h5tools_str_append(&buffer, "%s", buf);
             h5tools_str_append(&buffer, "}");
             h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols,
                                    (hsize_t)0, (hsize_t)0);
@@ -2371,11 +2367,11 @@ list_lnk(const char *name, const H5L_info2_t *linfo, void *_iter)
                 goto done;
 
             h5tools_str_append(&buffer, "External Link {");
-            h5tools_str_append(&buffer, filename);
+            h5tools_str_append(&buffer, "%s", filename);
             h5tools_str_append(&buffer, "/");
             if (*path != '/')
                 h5tools_str_append(&buffer, "/");
-            h5tools_str_append(&buffer, path);
+            h5tools_str_append(&buffer, "%s", path);
             h5tools_str_append(&buffer, "}");
             h5tools_render_element(rawoutstream, info, &ctx, &buffer, &curr_pos, (size_t)info->line_ncols,
                                    (hsize_t)0, (hsize_t)0);
@@ -2526,7 +2522,7 @@ done:
  *              were borrowed from the GNU less(1).
  *
  * Return:      Success: Number of columns.
- *              Failure: Some default number of columms.
+ *              Failure: Some default number of columns.
  *-------------------------------------------------------------------------
  */
 static int
@@ -2646,7 +2642,7 @@ leave(int ret)
  *-------------------------------------------------------------------------
  */
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     hid_t              file_id = H5I_INVALID_HID;
     char *             fname = NULL, *oname = NULL, *x = NULL;
@@ -2722,9 +2718,9 @@ main(int argc, const char *argv[])
         }
         else if (!HDstrcmp(argv[argno], "--enable-error-stack")) {
             enable_error_stack = 1;
-            /* deprecated --errors */
         }
         else if (!HDstrcmp(argv[argno], "--errors")) {
+            /* deprecated --errors */
             enable_error_stack = 1;
         }
         else if (!HDstrcmp(argv[argno], "--follow-symlinks")) {
diff --git a/tools/src/h5perf/pio_engine.c b/tools/src/h5perf/pio_engine.c
index 3edc74a..1baaca2 100644
--- a/tools/src/h5perf/pio_engine.c
+++ b/tools/src/h5perf/pio_engine.c
@@ -282,7 +282,7 @@ do_pio(parameters param)
         /* Open file for write */
         char base_name[256];
 
-        HDsprintf(base_name, "#pio_tmp_%lu", nf);
+        HDsnprintf(base_name, sizeof(base_name), "#pio_tmp_%lu", nf);
         pio_create_filename(iot, base_name, fname, sizeof(fname));
         if (pio_debug_level > 0)
             HDfprintf(output, "rank %d: data filename=%s\n", pio_mpi_rank_g, fname);
@@ -420,7 +420,7 @@ pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t si
         /* If the prefix specifies the HDF5_PARAPREFIX directory, then
          * default to using the "/tmp/$USER" or "/tmp/$LOGIN"
          * directory instead. */
-        register char *user, *login, *subdir;
+        char *user, *login, *subdir;
 
         user   = HDgetenv("USER");
         login  = HDgetenv("LOGIN");
@@ -898,7 +898,7 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nby
                     }     /* end if */
                 }         /* end else */
 
-                HDsprintf(dname, "Dataset_%ld", ndset);
+                HDsnprintf(dname, sizeof(dname), "Dataset_%ld", ndset);
                 h5ds_id = H5DCREATE(fd->h5fd, dname, ELMT_H5_TYPE, h5dset_space_id, h5dcpl);
 
                 if (h5ds_id < 0) {
@@ -1879,7 +1879,7 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nbyt
                 break;
 
             case PHDF5:
-                HDsprintf(dname, "Dataset_%ld", ndset);
+                HDsnprintf(dname, sizeof(dname), "Dataset_%ld", ndset);
                 h5ds_id = H5DOPEN(fd->h5fd, dname);
                 if (h5ds_id < 0) {
                     HDfprintf(stderr, "HDF5 Dataset open failed\n");
diff --git a/tools/src/h5perf/pio_perf.c b/tools/src/h5perf/pio_perf.c
index bf5f62f..003c4f2 100644
--- a/tools/src/h5perf/pio_perf.c
+++ b/tools/src/h5perf/pio_perf.c
@@ -188,7 +188,7 @@ typedef struct _minmax {
 
 /* local functions */
 static off_t           parse_size_directive(const char *size);
-static struct options *parse_command_line(int argc, char *argv[]);
+static struct options *parse_command_line(int argc, const char *const *argv);
 static void            run_test_loop(struct options *options);
 static int             run_test(iotype iot, parameters parms, struct options *opts);
 static void            output_all_info(minmax *mm, int count, int indent_level);
@@ -200,7 +200,7 @@ static void  output_results(const struct options *options, const char *name, min
                             off_t data_size);
 static void  output_times(const struct options *options, const char *name, minmax *table, int table_size);
 static void  output_report(const char *fmt, ...);
-static void  print_indent(register int indent);
+static void  print_indent(int indent);
 static void  usage(const char *prog);
 static void  report_parameters(struct options *opts);
 static off_t squareo(off_t);
@@ -260,7 +260,7 @@ main(int argc, char *argv[])
     pio_comm_g = MPI_COMM_WORLD;
 
     h5_set_info_object();
-    opts = parse_command_line(argc, argv);
+    opts = parse_command_line(argc, (const char *const *)argv);
 
     if (!opts) {
         exit_value = EXIT_FAILURE;
@@ -336,7 +336,7 @@ run_test_loop(struct options *opts)
     /* start with max_num_procs and decrement it by half for each loop. */
     /* if performance needs restart, fewer processes may be needed. */
     for (num_procs = opts->max_num_procs; num_procs >= opts->min_num_procs; num_procs >>= 1) {
-        register size_t buf_size;
+        size_t buf_size;
 
         parms.num_procs = num_procs;
 
@@ -411,34 +411,34 @@ run_test_loop(struct options *opts)
 static int
 run_test(iotype iot, parameters parms, struct options *opts)
 {
-    results      res;
-    register int i, ret_value = SUCCESS;
-    int          comm_size;
-    off_t        raw_size;
-    minmax *     write_mpi_mm_table   = NULL;
-    minmax *     write_mm_table       = NULL;
-    minmax *     write_gross_mm_table = NULL;
-    minmax *     write_raw_mm_table   = NULL;
-    minmax *     read_mpi_mm_table    = NULL;
-    minmax *     read_mm_table        = NULL;
-    minmax *     read_gross_mm_table  = NULL;
-    minmax *     read_raw_mm_table    = NULL;
-    minmax *     read_open_mm_table   = NULL;
-    minmax *     read_close_mm_table  = NULL;
-    minmax *     write_open_mm_table  = NULL;
-    minmax *     write_close_mm_table = NULL;
-    minmax       write_mpi_mm         = {0.0, 0.0, 0.0, 0};
-    minmax       write_mm             = {0.0, 0.0, 0.0, 0};
-    minmax       write_gross_mm       = {0.0, 0.0, 0.0, 0};
-    minmax       write_raw_mm         = {0.0, 0.0, 0.0, 0};
-    minmax       read_mpi_mm          = {0.0, 0.0, 0.0, 0};
-    minmax       read_mm              = {0.0, 0.0, 0.0, 0};
-    minmax       read_gross_mm        = {0.0, 0.0, 0.0, 0};
-    minmax       read_raw_mm          = {0.0, 0.0, 0.0, 0};
-    minmax       read_open_mm         = {0.0, 0.0, 0.0, 0};
-    minmax       read_close_mm        = {0.0, 0.0, 0.0, 0};
-    minmax       write_open_mm        = {0.0, 0.0, 0.0, 0};
-    minmax       write_close_mm       = {0.0, 0.0, 0.0, 0};
+    results res;
+    int     i, ret_value = SUCCESS;
+    int     comm_size;
+    off_t   raw_size;
+    minmax *write_mpi_mm_table   = NULL;
+    minmax *write_mm_table       = NULL;
+    minmax *write_gross_mm_table = NULL;
+    minmax *write_raw_mm_table   = NULL;
+    minmax *read_mpi_mm_table    = NULL;
+    minmax *read_mm_table        = NULL;
+    minmax *read_gross_mm_table  = NULL;
+    minmax *read_raw_mm_table    = NULL;
+    minmax *read_open_mm_table   = NULL;
+    minmax *read_close_mm_table  = NULL;
+    minmax *write_open_mm_table  = NULL;
+    minmax *write_close_mm_table = NULL;
+    minmax  write_mpi_mm         = {0.0, 0.0, 0.0, 0};
+    minmax  write_mm             = {0.0, 0.0, 0.0, 0};
+    minmax  write_gross_mm       = {0.0, 0.0, 0.0, 0};
+    minmax  write_raw_mm         = {0.0, 0.0, 0.0, 0};
+    minmax  read_mpi_mm          = {0.0, 0.0, 0.0, 0};
+    minmax  read_mm              = {0.0, 0.0, 0.0, 0};
+    minmax  read_gross_mm        = {0.0, 0.0, 0.0, 0};
+    minmax  read_raw_mm          = {0.0, 0.0, 0.0, 0};
+    minmax  read_open_mm         = {0.0, 0.0, 0.0, 0};
+    minmax  read_close_mm        = {0.0, 0.0, 0.0, 0};
+    minmax  write_open_mm        = {0.0, 0.0, 0.0, 0};
+    minmax  write_close_mm       = {0.0, 0.0, 0.0, 0};
 
     raw_size      = parms.num_files * (off_t)parms.num_dsets * (off_t)parms.num_bytes;
     parms.io_type = iot;
@@ -1098,10 +1098,9 @@ output_report(const char *fmt, ...)
  *              things.
  * Return:      Nothing
  * Programmer:  Bill Wendling, 29. October 2001
- * Modifications:
  */
 static void
-print_indent(register int indent)
+print_indent(int indent)
 {
     int myrank;
 
@@ -1276,9 +1275,9 @@ report_parameters(struct options *opts)
  *    Added 2D testing (Christian Chilan, 10. August 2005)
  */
 static struct options *
-parse_command_line(int argc, char *argv[])
+parse_command_line(int argc, const char *const *argv)
 {
-    register int    opt;
+    int             opt;
     struct options *cl_opts;
 
     cl_opts = (struct options *)malloc(sizeof(struct options));
@@ -1305,7 +1304,7 @@ parse_command_line(int argc, char *argv[])
     cl_opts->h5_write_only = FALSE; /* Do both read and write by default */
     cl_opts->verify        = FALSE; /* No Verify data correctness by default */
 
-    while ((opt = H5_get_option(argc, (const char **)argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             case 'a':
                 cl_opts->h5_alignment = parse_size_directive(H5_optarg);
diff --git a/tools/src/h5perf/sio_engine.c b/tools/src/h5perf/sio_engine.c
index 98cb920..bdd2c08 100644
--- a/tools/src/h5perf/sio_engine.c
+++ b/tools/src/h5perf/sio_engine.c
@@ -328,7 +328,7 @@ sio_create_filename(iotype iot, const char *base_name, char *fullname, size_t si
         /* If the prefix specifies the HDF5_PREFIX directory, then
          * default to using the "/tmp/$USER" or "/tmp/$LOGIN"
          * directory instead. */
-        register char *user, *login, *subdir;
+        char *user, *login, *subdir;
 
         user   = HDgetenv("USER");
         login  = HDgetenv("LOGIN");
@@ -1267,7 +1267,7 @@ done:
 static void
 do_cleanupfile(iotype iot, char *filename)
 {
-    char  temp[2048];
+    char  temp[4096 + sizeof("-?.h5")];
     int   j;
     hid_t driver;
 
diff --git a/tools/src/h5perf/sio_perf.c b/tools/src/h5perf/sio_perf.c
index 0eb4508..dc2e15e 100644
--- a/tools/src/h5perf/sio_perf.c
+++ b/tools/src/h5perf/sio_perf.c
@@ -164,7 +164,7 @@ typedef struct {
 
 /* local functions */
 static hsize_t         parse_size_directive(const char *size);
-static struct options *parse_command_line(int argc, const char *argv[]);
+static struct options *parse_command_line(int argc, const char *const *argv);
 static void            run_test_loop(struct options *options);
 static int             run_test(iotype iot, parameters parms, struct options *opts);
 static void            output_all_info(minmax *mm, int count, int indent_level);
@@ -173,7 +173,7 @@ static void            accumulate_minmax_stuff(const minmax *mm, int count, minm
 static void output_results(const struct options *options, const char *name, minmax *table, int table_size,
                            off_t data_size);
 static void output_report(const char *fmt, ...);
-static void print_indent(register int indent);
+static void print_indent(int indent);
 static void usage(const char *prog);
 static void report_parameters(struct options *opts);
 
@@ -185,7 +185,7 @@ static void report_parameters(struct options *opts);
  * Modifications:
  */
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     int             exit_value = EXIT_SUCCESS;
     struct options *opts       = NULL;
@@ -197,7 +197,7 @@ main(int argc, const char *argv[])
 
     output = stdout;
 
-    opts = parse_command_line(argc, argv);
+    opts = parse_command_line(argc, (const char *const *)argv);
 
     if (!opts) {
         exit_value = EXIT_FAILURE;
@@ -277,7 +277,7 @@ run_test_loop(struct options *opts)
     }
 
     /* print size information */
-    output_report("Transfer Buffer Size (bytes): %d\n", buf_bytes);
+    output_report("Transfer Buffer Size (bytes): %zu\n", buf_bytes);
     output_report("File Size(MB): %.2f\n", ((double)parms.num_bytes) / ONE_MB);
 
     print_indent(0);
@@ -299,25 +299,25 @@ run_test_loop(struct options *opts)
 static int
 run_test(iotype iot, parameters parms, struct options *opts)
 {
-    results      res;
-    register int i, ret_value = SUCCESS;
-    off_t        raw_size;
-    minmax *     write_sys_mm_table   = NULL;
-    minmax *     write_mm_table       = NULL;
-    minmax *     write_gross_mm_table = NULL;
-    minmax *     write_raw_mm_table   = NULL;
-    minmax *     read_sys_mm_table    = NULL;
-    minmax *     read_mm_table        = NULL;
-    minmax *     read_gross_mm_table  = NULL;
-    minmax *     read_raw_mm_table    = NULL;
-    minmax       write_sys_mm         = {0.0, 0.0, 0.0, 0};
-    minmax       write_mm             = {0.0, 0.0, 0.0, 0};
-    minmax       write_gross_mm       = {0.0, 0.0, 0.0, 0};
-    minmax       write_raw_mm         = {0.0, 0.0, 0.0, 0};
-    minmax       read_sys_mm          = {0.0, 0.0, 0.0, 0};
-    minmax       read_mm              = {0.0, 0.0, 0.0, 0};
-    minmax       read_gross_mm        = {0.0, 0.0, 0.0, 0};
-    minmax       read_raw_mm          = {0.0, 0.0, 0.0, 0};
+    results res;
+    int     i, ret_value = SUCCESS;
+    off_t   raw_size;
+    minmax *write_sys_mm_table   = NULL;
+    minmax *write_mm_table       = NULL;
+    minmax *write_gross_mm_table = NULL;
+    minmax *write_raw_mm_table   = NULL;
+    minmax *read_sys_mm_table    = NULL;
+    minmax *read_mm_table        = NULL;
+    minmax *read_gross_mm_table  = NULL;
+    minmax *read_raw_mm_table    = NULL;
+    minmax  write_sys_mm         = {0.0, 0.0, 0.0, 0};
+    minmax  write_mm             = {0.0, 0.0, 0.0, 0};
+    minmax  write_gross_mm       = {0.0, 0.0, 0.0, 0};
+    minmax  write_raw_mm         = {0.0, 0.0, 0.0, 0};
+    minmax  read_sys_mm          = {0.0, 0.0, 0.0, 0};
+    minmax  read_mm              = {0.0, 0.0, 0.0, 0};
+    minmax  read_gross_mm        = {0.0, 0.0, 0.0, 0};
+    minmax  read_raw_mm          = {0.0, 0.0, 0.0, 0};
 
     raw_size      = (off_t)parms.num_bytes;
     parms.io_type = iot;
@@ -657,10 +657,9 @@ output_report(const char *fmt, ...)
  *              things.
  * Return:      Nothing
  * Programmer:  Bill Wendling, 29. October 2001
- * Modifications:
  */
 static void
-print_indent(register int indent)
+print_indent(int indent)
 {
     indent *= TAB_SPACE;
 
@@ -817,7 +816,7 @@ report_parameters(struct options *opts)
  *    Added multidimensional testing (Christian Chilan, April, 2008)
  */
 static struct options *
-parse_command_line(int argc, const char *argv[])
+parse_command_line(int argc, const char *const *argv)
 {
     int             opt;
     struct options *cl_opts;
diff --git a/tools/src/h5repack/PARALLEL_REPACK_readme.txt b/tools/src/h5repack/PARALLEL_REPACK_readme.txt
index a8e703e..0b9783a 100644
--- a/tools/src/h5repack/PARALLEL_REPACK_readme.txt
+++ b/tools/src/h5repack/PARALLEL_REPACK_readme.txt
@@ -64,7 +64,7 @@ of a parallel version of repack. A quick summary of this is discussion follows:
 
   Q5. Can you collectively copy data using hyperslab selections
       rather than having each MPI rank copy the data from the
-      input dataset to the ouput dataset?
+      input dataset to the output dataset?
   A5. Probably yes.  I can look at implementing this improvement
       in the current design.
 
diff --git a/tools/src/h5repack/create_h5file.c b/tools/src/h5repack/create_h5file.c
index 5efa325..910a2d4 100644
--- a/tools/src/h5repack/create_h5file.c
+++ b/tools/src/h5repack/create_h5file.c
@@ -207,13 +207,13 @@ create_attributes(hid_t group_id)
         }
 
         if (H5Aclose(attr_id) < 0) {
-            fprintf(stderr, "failed to close the attribure\n");
+            fprintf(stderr, "failed to close the attribute\n");
             goto error;
         }
     }
 
     if (H5Sclose(attr_space) < 0) {
-        fprintf(stderr, "failed to close the attribure space\n");
+        fprintf(stderr, "failed to close the attribute space\n");
         goto error;
     }
 
diff --git a/tools/src/h5repack/h5prepack_main.c b/tools/src/h5repack/h5prepack_main.c
index 78f174c..56754a4 100644
--- a/tools/src/h5repack/h5prepack_main.c
+++ b/tools/src/h5repack/h5prepack_main.c
@@ -40,13 +40,13 @@ static struct h5_long_options l_opts[] = {{"alignment", require_arg, 'a'},
                                           {"file", require_arg, 'e'},
                                           {"filter", require_arg, 'f'},
                                           {"help", no_arg, 'h'},
-                                          {"infile", require_arg, 'i'}, /* for backward compability */
+                                          {"infile", require_arg, 'i'}, /* for backward compatibility */
                                           {"low", require_arg, 'j'},
                                           {"high", require_arg, 'k'},
                                           {"layout", require_arg, 'l'},
                                           {"minimum", require_arg, 'm'},
                                           {"native", no_arg, 'n'},
-                                          {"outfile", require_arg, 'o'}, /* for backward compability */
+                                          {"outfile", require_arg, 'o'}, /* for backward compatibility */
                                           {"sort_by", require_arg, 'q'},
                                           {"ssize", require_arg, 's'},
                                           {"threshold", require_arg, 't'},
@@ -380,7 +380,7 @@ read_info(const char *filename, pack_opt_t *options)
             goto done;
         }
 
-        /* find begining of info */
+        /* find beginning of info */
         i = 0;
         c = '0';
         while (c != ' ') {
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index a938fd6..60b3967 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -894,7 +894,7 @@ select_objs_by_rank(hid_t fidin, trav_table_t *orig, int **table_index)
         for (k = 0; k < (int)orig->nobjs; k++) {
             int mod_rank = (int)((int)k % g_nTasks);
 
-            /* For debugging only, make it alwasy true - Ray */
+            /* For debugging only, make it always true - Ray */
             // orig->objs[k].use_hyperslab = true;
 
             if ((orig->objs[k].use_hyperslab) || (mod_rank == (int)g_nID)) {
@@ -1633,7 +1633,7 @@ pcopy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt, int *obj_index, in
                     // read_time  = 0.0;
                     write_time = 0.0;
 
-                    /* Potentially override the default size where we will transistion
+                    /* Potentially override the default size where we will transition
                      * to using hyperslab selections to divide the work between mpi ranks.
                      */
 
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index 0a26500..a805b3d 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -18,7 +18,7 @@
 /* Name of tool */
 #define PROGRAMNAME "h5repack"
 
-static int  parse_command_line(int argc, const char **argv, pack_opt_t *options);
+static int  parse_command_line(int argc, const char *const *argv, pack_opt_t *options);
 static void leave(int ret) H5_ATTR_NORETURN;
 
 /* module-scoped variables */
@@ -31,7 +31,7 @@ const char *outfile = NULL;
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *s_opts = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:v*z:EG:LM:P:S:T:VXWY:Z:1:2:3:4:5:6:7:8:9:0:";
+static const char *s_opts = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:v*z:E*G:LM:P:S:T:VXWY:Z:1:2:3:4:5:6:7:8:9:0:";
 static struct h5_long_options l_opts[] = {{"alignment", require_arg, 'a'},
                                           {"block", require_arg, 'b'},
                                           {"compact", require_arg, 'c'},
@@ -52,7 +52,7 @@ static struct h5_long_options l_opts[] = {{"alignment", require_arg, 'a'},
                                           {"ublock", require_arg, 'u'},
                                           {"verbose", optional_arg, 'v'},
                                           {"sort_order", require_arg, 'z'},
-                                          {"enable-error-stack", no_arg, 'E'},
+                                          {"enable-error-stack", optional_arg, 'E'},
                                           {"fs_pagesize", require_arg, 'G'},
                                           {"latest", no_arg, 'L'},
                                           {"metadata_block_size", require_arg, 'M'},
@@ -92,6 +92,11 @@ usage(const char *prog)
     PRINTSTREAM(rawoutstream, "usage: %s [OPTIONS] file1 file2\n", prog);
     PRINTVALSTREAM(rawoutstream, "  file1                    Input HDF5 File\n");
     PRINTVALSTREAM(rawoutstream, "  file2                    Output HDF5 File\n");
+    PRINTVALSTREAM(rawoutstream, "  ERROR\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "   --enable-error-stack    Prints messages from the HDF5 error stack as they occur.\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "                           Optional value 2 also prints file open errors.\n");
     PRINTVALSTREAM(rawoutstream, "  OPTIONS\n");
     PRINTVALSTREAM(rawoutstream, "   -h, --help              Print a usage message and exit\n");
     PRINTVALSTREAM(rawoutstream, "   -v N, --verbose=N       Verbose mode, print object information.\n");
@@ -99,9 +104,6 @@ usage(const char *prog)
     PRINTVALSTREAM(rawoutstream, "   -V, --version           Print version number and exit\n");
     PRINTVALSTREAM(rawoutstream, "   -n, --native            Use a native HDF5 type when repacking\n");
     PRINTVALSTREAM(rawoutstream,
-                   "   --enable-error-stack    Prints messages from the HDF5 error stack as they\n");
-    PRINTVALSTREAM(rawoutstream, "                           occur\n");
-    PRINTVALSTREAM(rawoutstream,
                    "   --src-vol-value         Value (ID) of the VOL connector to use for opening the\n");
     PRINTVALSTREAM(rawoutstream, "                           input HDF5 file specified\n");
     PRINTVALSTREAM(rawoutstream,
@@ -507,7 +509,7 @@ set_sort_order(const char *form)
  *-------------------------------------------------------------------------
  */
 static int
-parse_command_line(int argc, const char **argv, pack_opt_t *options)
+parse_command_line(int argc, const char *const *argv, pack_opt_t *options)
 {
     h5tools_vol_info_t in_vol_info;
     h5tools_vol_info_t out_vol_info;
@@ -701,7 +703,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
             case 'a':
                 options->alignment = HDstrtoull(H5_optarg, NULL, 0);
                 if (options->alignment < 1) {
-                    error_msg("invalid alignment size\n", H5_optarg);
+                    error_msg("invalid alignment size `%s`\n", H5_optarg);
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
                     goto done;
@@ -721,7 +723,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
                 else if (!HDstrcmp(strategy, "NONE"))
                     options->fs_strategy = H5F_FSPACE_STRATEGY_NONE;
                 else {
-                    error_msg("invalid file space management strategy\n", H5_optarg);
+                    error_msg("invalid file space management strategy `%s`\n", H5_optarg);
                     h5tools_setstatus(EXIT_FAILURE);
                     ret_value = -1;
                     goto done;
@@ -771,7 +773,10 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
                 break;
 
             case 'E':
-                enable_error_stack = 1;
+                if (H5_optarg != NULL)
+                    enable_error_stack = HDatoi(H5_optarg);
+                else
+                    enable_error_stack = 1;
                 break;
 
             case '1':
@@ -928,7 +933,7 @@ done:
  *-------------------------------------------------------------------------
  */
 int
-main(int argc, const char **argv)
+main(int argc, char **argv)
 {
     pack_opt_t options; /*the global options */
     int        parse_ret;
@@ -958,7 +963,7 @@ main(int argc, const char **argv)
     /* Initialize default indexing options */
     sort_by = H5_INDEX_CRT_ORDER;
 
-    parse_ret = parse_command_line(argc, argv, &options);
+    parse_ret = parse_command_line(argc, (const char *const *)argv, &options);
     if (parse_ret < 0) {
         HDprintf("Error occurred while parsing command-line options\n");
         h5tools_setstatus(EXIT_FAILURE);
diff --git a/tools/src/h5stat/h5stat.c b/tools/src/h5stat/h5stat.c
index 6b01e49..e42af10 100644
--- a/tools/src/h5stat/h5stat.c
+++ b/tools/src/h5stat/h5stat.c
@@ -169,7 +169,7 @@ struct handler_t {
     char **obj;
 };
 
-static const char *s_opts = "Aa:Ddm:EFfhGgl:sSTO:Vw:H:";
+static const char *s_opts = "Aa:Ddm:E*FfhGgl:sSTO:Vw:H:";
 /* e.g. "filemetadata" has to precede "file"; "groupmetadata" has to precede "group" etc. */
 static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
                                           {"filemetadata", no_arg, 'F'},
@@ -181,7 +181,7 @@ static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
                                           {"object", require_arg, 'O'},
                                           {"version", no_arg, 'V'},
                                           {"attribute", no_arg, 'A'},
-                                          {"enable-error-stack", no_arg, 'E'},
+                                          {"enable-error-stack", optional_arg, 'E'},
                                           {"numattrs", require_arg, 'a'},
                                           {"freespace", no_arg, 's'},
                                           {"summary", no_arg, 'S'},
@@ -211,6 +211,9 @@ usage(const char *prog)
     HDfflush(stdout);
     HDfprintf(stdout, "Usage: %s [OPTIONS] file\n", prog);
     HDfprintf(stdout, "\n");
+    HDfprintf(stdout, "      ERROR\n");
+    HDfprintf(stdout, "     --enable-error-stack  Prints messages from the HDF5 error stack as they occur\n");
+    HDfprintf(stdout, "                           Optional value 2 also prints file open errors\n");
     HDfprintf(stdout, "      OPTIONS\n");
     HDfprintf(stdout, "     -h, --help            Print a usage message and exit\n");
     HDfprintf(stdout, "     -V, --version         Print version number and exit\n");
@@ -235,7 +238,6 @@ usage(const char *prog)
     HDfprintf(stdout, "                           than 0.  The default threshold is 10.\n");
     HDfprintf(stdout, "     -s, --freespace       Print free space information\n");
     HDfprintf(stdout, "     -S, --summary         Print summary of file space information\n");
-    HDfprintf(stdout, "     --enable-error-stack  Prints messages from the HDF5 error stack as they occur\n");
     HDfprintf(stdout, "     --s3-cred=<cred>      Access file on S3, using provided credential\n");
     HDfprintf(stdout, "                           <cred> :: (region,id,key)\n");
     HDfprintf(stdout, "                           If <cred> == \"(,,)\", no authentication is used.\n");
@@ -830,7 +832,7 @@ hand_free(struct handler_t *hand)
  *-------------------------------------------------------------------------
  */
 static int
-parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
+parse_command_line(int argc, const char *const *argv, struct handler_t **hand_ret)
 {
     int               opt;
     unsigned          u;
@@ -852,7 +854,10 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
                 break;
 
             case 'E':
-                enable_error_stack = 1;
+                if (H5_optarg != NULL)
+                    enable_error_stack = HDatoi(H5_optarg);
+                else
+                    enable_error_stack = 1;
                 break;
 
             case 'F':
@@ -1677,7 +1682,7 @@ print_statistics(const char *name, const iter_t *iter)
  *-------------------------------------------------------------------------
  */
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     iter_t            iter;
     const char *      fname   = NULL;
@@ -1693,7 +1698,7 @@ main(int argc, const char *argv[])
 
     HDmemset(&iter, 0, sizeof(iter));
 
-    if (parse_command_line(argc, argv, &hand) < 0)
+    if (parse_command_line(argc, (const char *const *)argv, &hand) < 0)
         goto done;
 
     /* enable error reporting if command line option */
@@ -1736,7 +1741,7 @@ main(int argc, const char *argv[])
             warn_msg("Unable to retrieve file size\n");
         HDassert(iter.filesize != 0);
 
-        /* Get storge info for file-level structures */
+        /* Get storage info for file-level structures */
         if (H5Fget_info2(fid, &finfo) < 0)
             warn_msg("Unable to retrieve file info\n");
         else {
diff --git a/tools/src/misc/h5clear.c b/tools/src/misc/h5clear.c
index face2f0..15c170d 100644
--- a/tools/src/misc/h5clear.c
+++ b/tools/src/misc/h5clear.c
@@ -109,7 +109,7 @@ usage(const char *prog)
  *-------------------------------------------------------------------------
  */
 static int
-parse_command_line(int argc, const char **argv)
+parse_command_line(int argc, const char *const *argv)
 {
     int opt;
 
@@ -224,7 +224,7 @@ leave(int ret)
  *-------------------------------------------------------------------------
  */
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     char *   fname = NULL;            /* File name */
     hid_t    fapl  = H5I_INVALID_HID; /* File access property list */
@@ -240,7 +240,7 @@ main(int argc, const char *argv[])
     h5tools_init();
 
     /* Parse command line options */
-    if (parse_command_line(argc, argv) < 0)
+    if (parse_command_line(argc, (const char *const *)argv) < 0)
         goto done;
 
     if (fname_g == NULL)
diff --git a/tools/src/misc/h5delete.c b/tools/src/misc/h5delete.c
index 3c4f8d5..20e81a1 100644
--- a/tools/src/misc/h5delete.c
+++ b/tools/src/misc/h5delete.c
@@ -29,7 +29,7 @@ usage(void)
 }
 
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     hbool_t     quiet = FALSE;
     const char *name  = NULL;
diff --git a/tools/src/misc/h5mkgrp.c b/tools/src/misc/h5mkgrp.c
index 1e66fce..1b8b23d 100644
--- a/tools/src/misc/h5mkgrp.c
+++ b/tools/src/misc/h5mkgrp.c
@@ -131,7 +131,7 @@ usage(const char *prog)
  *-------------------------------------------------------------------------
  */
 static int
-parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options)
+parse_command_line(int argc, const char *const *argv, mkgrp_opt_t *options)
 {
     int                opt;        /* Option from command line */
     size_t             curr_group; /* Current group name to copy */
@@ -281,7 +281,7 @@ parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options)
  *-------------------------------------------------------------------------
  */
 int
-main(int argc, const char *argv[])
+main(int argc, char *argv[])
 {
     hid_t  fid     = H5I_INVALID_HID; /* HDF5 file ID */
     hid_t  lcpl_id = H5I_INVALID_HID; /* Link creation property list ID */
@@ -303,7 +303,7 @@ main(int argc, const char *argv[])
     }
 
     /* Parse command line */
-    if (parse_command_line(argc, argv, &params_g) < 0) {
+    if (parse_command_line(argc, (const char *const *)argv, &params_g) < 0) {
         error_msg("unable to parse command line arguments\n");
         leave(EXIT_FAILURE);
     }