Sprinkle H5_ATTR_FORMAT over printf(3)-like functions in tools and fix issues (#1423)

* Correct some conversion specifications.

* Replace many "%lld" occurrences with "%" PRIuHSIZE except for a few
instances where PRIdHSIZE was appropriate.  Remove a couple of casts and
use correct format strings, instead.

* Copy values from a possibly unaligned buffer to aligned local variables
instead of casting and dereferencing pointers into the buffer.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

5 files changed, 44 insertions, 47 deletions

diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c
index 5f64d6c..827daf3 100644
--- a/tools/src/h5dump/h5dump_xml.c
+++ b/tools/src/h5dump/h5dump_xml.c
@@ -1779,8 +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);
@@ -1790,10 +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);
                 }
@@ -1802,10 +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);
                 }
@@ -3897,8 +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);
             }
@@ -4529,12 +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 b9572fe..50d0f5d 100644
--- a/tools/src/h5format_convert/h5format_convert.c
+++ b/tools/src/h5format_convert/h5format_convert.c
@@ -127,7 +127,7 @@ parse_command_line(int argc, const char *const *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;
                 }
diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c
index 0d34574..a27a8cc 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;
diff --git a/tools/src/h5perf/pio_perf.c b/tools/src/h5perf/pio_perf.c
index c233684..7e12bed 100644
--- a/tools/src/h5perf/pio_perf.c
+++ b/tools/src/h5perf/pio_perf.c
@@ -199,7 +199,7 @@ static int             destroy_comm_world(void);
 static void  output_results(const struct options *options, const char *name, minmax *table, int table_size,
                             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  output_report(const char *fmt, ...) H5_ATTR_FORMAT(printf, 1, 2);
 static void  print_indent(register int indent);
 static void  usage(const char *prog);
 static void  report_parameters(struct options *opts);
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index 68e37fd..4c88bd7 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -701,7 +701,7 @@ parse_command_line(int argc, const char *const *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 +721,7 @@ parse_command_line(int argc, const char *const *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;