1 10 Merges from develop (#424)

* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merge updates

#358 patches from vtk
#361 fix header guard spelling

* format fix

* Fix missing underscore and make H5public.h closer to dev

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup

* format alignment

* Add missing test ref file

14 files changed, 94 insertions, 72 deletions

diff --git a/tools/lib/h5diff.h b/tools/lib/h5diff.h
index d518675..f14bcda 100644
--- a/tools/lib/h5diff.h
+++ b/tools/lib/h5diff.h
@@ -11,8 +11,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef H5DIFF_H__
-#define H5DIFF_H__
+#ifndef H5DIFF_H
+#define H5DIFF_H
 
 #include "hdf5.h"
 #include "h5tools.h"
@@ -159,4 +159,4 @@ int  print_objname(diff_opt_t *opts, hsize_t nfound);
 void do_print_objname(const char *OBJ, const char *path1, const char *path2, diff_opt_t *opts);
 void do_print_attrname(const char *attr, const char *path1, const char *path2);
 
-#endif /* H5DIFF_H__ */
+#endif /* H5DIFF_H */
diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index 9db045f..bd4470b 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -3133,48 +3133,66 @@ print_pos(diff_opt_t *opts, hsize_t idx, size_t u)
             hsize_t curr_pos = idx;
 
             parallel_print("[ ");
-            H5TOOLS_DEBUG("do calc_acc_pos[%ld] nelmts:%d - errstat:%d", i, opts->hs_nelmts, opts->err_stat);
+            H5TOOLS_DEBUG("do calc_acc_pos[%ld] nelmts:%d - errstat:%d", idx, opts->hs_nelmts,
+                          opts->err_stat);
 
             if (opts->sset[0] != NULL) {
                 /* Subsetting is used - calculate total position */
-                hsize_t elmnt_cnt = 1;
-                hsize_t dim_cnt   = 0;   /* previous dim size */
-                hsize_t str_cnt   = 0;   /* previous dim stride */
-                hsize_t curr_idx  = idx; /* calculated running position */
-                hsize_t str_idx   = 0;
-                hsize_t blk_idx   = 0;
-                hsize_t cnt_idx   = 0;
-                hsize_t hs_idx    = 0;
-                j                 = opts->rank - 1;
+                hsize_t prev_dim_size = 0; /* previous dim size */
+                hsize_t prev_str      = 0; /* previouw stride idx*/
+                hsize_t str_cnt       = 0; /* stride multiplier*/
+                hsize_t curr_idx      = 0; /* calculated running position */
+                hsize_t str_idx       = 0;
+                hsize_t blk_idx       = 0;
+                hsize_t cnt_idx       = 0;
+                hsize_t dim_size      = 0; /* current dim size */
+                hsize_t elmnt_cnt     = 1;
+                hsize_t next_idx      = idx;
+                hsize_t data_idx      = 0;
+                j                     = opts->rank - 1;
+                H5TOOLS_DEBUG("...begin:%ld=> opts->rank:%ld (idx:%ld)", j, opts->rank, idx);
                 do {
-                    cnt_idx = opts->sset[0]->count.data[j]; /* Count value for current dim */
-                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - count:%ld", j,
-                                  curr_pos, curr_idx, cnt_idx);
-                    blk_idx = opts->sset[0]->block.data[j]; /* Block value for current dim */
-                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - block:%ld", j,
-                                  curr_pos, curr_idx, blk_idx);
-                    hs_idx = cnt_idx * blk_idx; /* hyperslab area value for current dim */
-                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - hs:%ld", j, curr_pos,
-                                  curr_idx, hs_idx);
-                    str_idx = opts->sset[0]->stride.data[j]; /* Stride value for current dim */
-                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - stride:%ld", j,
-                                  curr_pos, curr_idx, str_idx);
-                    elmnt_cnt *= opts->dims[j]; /* Total number of elements in dimension */
-                    H5TOOLS_DEBUG("... sset loop:%d with elmnt_cnt:%ld", j, elmnt_cnt);
-                    if (str_idx > blk_idx)
-                        curr_idx += dim_cnt * (str_idx - blk_idx); /* */
-                    else if (curr_idx >= hs_idx)
-                        curr_idx += dim_cnt * str_cnt;
-                    H5TOOLS_DEBUG("... sset loop:%d with idx:%ld (curr_idx:%ld) - stride:%ld", j, idx,
-                                  curr_idx, str_idx);
-                    dim_cnt = elmnt_cnt; /* */
-                    if (str_idx > blk_idx)
-                        str_cnt = str_idx - blk_idx; /* */
-                    else
-                        str_cnt = str_idx; /* */
-                    H5TOOLS_DEBUG("... sset loop:%d with dim_cnt:%ld - str_cnt:%ld", j, dim_cnt, str_cnt);
+                    curr_idx = next_idx;                      /* New current data position */
+                    cnt_idx  = opts->sset[0]->count.data[j];  /* Count value for current dim */
+                    blk_idx  = opts->sset[0]->block.data[j];  /* Block value for current dim */
+                    str_idx  = opts->sset[0]->stride.data[j]; /* Stride value for current dim */
+                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - c:%ld b:%ld s:%ld", j,
+                                  curr_pos, curr_idx, cnt_idx, blk_idx, str_idx);
+                    dim_size = opts->dims[j]; /* Current dimension size */
+                    // elmnt_cnt *= dim_size;    /* Total number of elements in dimension */
+                    H5TOOLS_DEBUG("... sset loop:%d with elmnt_cnt:%ld - (prev_dim_size:%ld - dim_size:%ld) "
+                                  "- str_cnt:%ld",
+                                  j, elmnt_cnt, prev_dim_size, dim_size, str_cnt);
+                    data_idx = elmnt_cnt * dim_size;
+                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (data_idx:%ld)", j, curr_pos, data_idx);
+                    for (i = 0; i < cnt_idx; i++) {
+                        H5TOOLS_DEBUG("... ... data loop:%d with cnt_idx:%ld - str_cnt:%ld (curr_idx:%ld - "
+                                      "data_idx:%ld)",
+                                      i, cnt_idx, str_cnt, curr_idx, data_idx);
+                        if (curr_idx >= data_idx) {
+                            /* get to next block */
+                            data_idx += str_idx * dim_size;
+                            /* get next block */
+                            str_cnt++;
+                            H5TOOLS_DEBUG(
+                                "... ... data loop:%d with cnt_idx:%ld - str_cnt:%ld - data_idx:%ld", i,
+                                cnt_idx, str_cnt, data_idx);
+                        }
+                        H5TOOLS_DEBUG("... ... end data loop:%d with dim_cnt:%ld - str_cnt:%ld - "
+                                      "(curr_idx:%ld - data_idx:%ld)",
+                                      i, dim_size, str_cnt, curr_idx, data_idx);
+                    }
+                    next_idx += dim_size * str_cnt; // + prev_dim_size;
+                    H5TOOLS_DEBUG("... sset loop:%d with curr_idx:%ld (next_idx:%ld)", j, curr_idx, next_idx);
+                    str_cnt       = 0;
+                    prev_str      = str_idx;
+                    prev_dim_size = dim_size;
+                    H5TOOLS_DEBUG("... end sset loop:%d with prev_dim_size:%ld (curr_idx:%ld - data_idx:%ld) "
+                                  "- str_cnt:%ld",
+                                  j, prev_dim_size, curr_idx, data_idx, str_cnt);
+                    elmnt_cnt *= dim_size; /* Total number of elements in dimension */
                     j--;
-                } while (curr_idx >= elmnt_cnt && j >= 0);
+                } while (next_idx >= elmnt_cnt && j >= 0);
                 curr_pos = curr_idx; /* New current position */
                 H5TOOLS_DEBUG("pos loop:%d,%d with  elmnt_cnt:%ld - curr_pos:%ld", i, j, elmnt_cnt, curr_pos);
             } /* if (opts->sset[0] != NULL) */
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index 90c6de5..baaf665 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -1599,7 +1599,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
         } break;
         case H5T_ARRAY: {
             int     k, ndims;
-            hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts;
+            hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts = 0;
             hid_t   memb = H5I_INVALID_HID;
 
             H5TOOLS_DEBUG("H5T_ARRAY");
diff --git a/tools/lib/h5tools.h b/tools/lib/h5tools.h
index 99a7500..53f16cf 100644
--- a/tools/lib/h5tools.h
+++ b/tools/lib/h5tools.h
@@ -17,8 +17,8 @@
  *
  * Purpose:     Support functions for the various tools.
  */
-#ifndef H5TOOLS_H__
-#define H5TOOLS_H__
+#ifndef H5TOOLS_H
+#define H5TOOLS_H
 
 #include "hdf5.h"
 #include "h5tools_error.h"
@@ -684,4 +684,4 @@ H5TOOLS_DLL hbool_t h5tools_render_region_element(FILE *stream, const h5tool_for
 }
 #endif
 
-#endif /* H5TOOLS_H__ */
+#endif /* H5TOOLS_H */
diff --git a/tools/lib/h5tools_dump.h b/tools/lib/h5tools_dump.h
index 9cebdc3..9b47789 100644
--- a/tools/lib/h5tools_dump.h
+++ b/tools/lib/h5tools_dump.h
@@ -14,8 +14,8 @@
 /*
  * Purpose:     Support h5dump functions for the various tools.
  */
-#ifndef H5TOOLS_DUMP_H__
-#define H5TOOLS_DUMP_H__
+#ifndef H5TOOLS_DUMP_H
+#define H5TOOLS_DUMP_H
 
 #include "h5tools_utils.h"
 
@@ -94,4 +94,4 @@ H5TOOLS_DLL void h5tools_print_packed_bits(h5tools_str_t *buffer /*in,out*/, hid
 }
 #endif
 
-#endif /* H5TOOLS_DUMP_H__ */
+#endif /* H5TOOLS_DUMP_H */
diff --git a/tools/lib/h5tools_error.h b/tools/lib/h5tools_error.h
index b8e5339..8fd33bb 100644
--- a/tools/lib/h5tools_error.h
+++ b/tools/lib/h5tools_error.h
@@ -14,8 +14,8 @@
 /*
  *  Header file for error values, etc.
  */
-#ifndef H5TOOLS_ERROR_H_
-#define H5TOOLS_ERROR_H_
+#ifndef H5TOOLS_ERROR_H
+#define H5TOOLS_ERROR_H
 
 #include "H5Epublic.h"
 #include "H5Eprivate.h" /* Error handling       */
@@ -250,4 +250,4 @@ H5TOOLS_DLLVAR hid_t H5E_tools_min_dbg_id_g;
         H5_LEAVE(ret_val)                                                                                    \
     } while (0)
 
-#endif /* H5TOOLS_ERROR_H_ */
+#endif /* H5TOOLS_ERROR_H */
diff --git a/tools/lib/h5tools_ref.h b/tools/lib/h5tools_ref.h
index 2720620..e3d55c6 100644
--- a/tools/lib/h5tools_ref.h
+++ b/tools/lib/h5tools_ref.h
@@ -11,8 +11,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef H5TOOLS_REF_H__
-#define H5TOOLS_REF_H__
+#ifndef H5TOOLS_REF_H
+#define H5TOOLS_REF_H
 
 #include "hdf5.h"
 
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index 7995d22..41a12d7 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -705,7 +705,7 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
                     long double templdouble;
 
                     HDmemcpy(&templdouble, vp, sizeof(long double));
-                    h5tools_str_append(str, OPT(info->fmt_double, "%Lf"), templdouble);
+                    h5tools_str_append(str, "%Lg", templdouble);
 #endif
                 }
                 break;
diff --git a/tools/lib/h5tools_str.h b/tools/lib/h5tools_str.h
index 1c3301a..3bbf6b1 100644
--- a/tools/lib/h5tools_str.h
+++ b/tools/lib/h5tools_str.h
@@ -15,8 +15,8 @@
  * Programmer:  Bill Wendling
  *              Monday, 19. February 2001
  */
-#ifndef H5TOOLS_STR_H__
-#define H5TOOLS_STR_H__
+#ifndef H5TOOLS_STR_H
+#define H5TOOLS_STR_H
 
 typedef struct h5tools_str_t {
     char * s;      /*allocate string       */
@@ -46,4 +46,4 @@ H5TOOLS_DLL char *h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *
                                      hid_t type, void *vp, h5tools_context_t *ctx);
 H5TOOLS_DLL char *h5tools_str_replace(const char *string, const char *substr, const char *replacement);
 
-#endif /* H5TOOLS_STR_H__ */
+#endif /* H5TOOLS_STR_H */
diff --git a/tools/lib/h5tools_utils.c b/tools/lib/h5tools_utils.c
index 3a68abe..108cd4f 100644
--- a/tools/lib/h5tools_utils.c
+++ b/tools/lib/h5tools_utils.c
@@ -196,7 +196,7 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
         /* long command line option */
         int        i;
         const char ch      = '=';
-        char *     arg     = &argv[opt_ind][2];
+        char *     arg     = HDstrdup(&argv[opt_ind][2]);
         size_t     arg_len = 0;
 
         opt_arg = strchr(&argv[opt_ind][2], ch);
@@ -251,6 +251,8 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
         opt_ind++;
         sp = 1;
+
+        HDfree(arg);
     }
     else {
         register char *cp; /* pointer into current token */
@@ -1077,12 +1079,14 @@ h5tools_parse_ros3_fapl_tuple(const char *tuple_str, int delim, H5FD_ros3_fapl_t
     ccred[1] = (const char *)s3cred[1];
     ccred[2] = (const char *)s3cred[2];
 
-    if (h5tools_populate_ros3_fapl(fapl_config_out, ccred) < 0)
+    if (0 == h5tools_populate_ros3_fapl(fapl_config_out, ccred))
         H5TOOLS_GOTO_ERROR(FAIL, "failed to populate S3 VFD FAPL config");
 
 done:
-    HDfree(s3cred);
-    HDfree(s3cred_src);
+    if (s3cred)
+        HDfree(s3cred);
+    if (s3cred_src)
+        HDfree(s3cred_src);
 
     return ret_value;
 }
diff --git a/tools/lib/h5tools_utils.h b/tools/lib/h5tools_utils.h
index d38abce..34ac89b 100644
--- a/tools/lib/h5tools_utils.h
+++ b/tools/lib/h5tools_utils.h
@@ -17,8 +17,8 @@
  *
  * Purpose:     Support functions for the various tools.
  */
-#ifndef H5TOOLS_UTILS_H__
-#define H5TOOLS_UTILS_H__
+#ifndef H5TOOLS_UTILS_H
+#define H5TOOLS_UTILS_H
 
 #include "hdf5.h"
 
@@ -190,4 +190,4 @@ H5TOOLS_DLL herr_t h5tools_parse_hdfs_fapl_tuple(const char *tuple_str, int deli
 }
 #endif
 
-#endif /* H5TOOLS_UTILS_H__ */
+#endif /* H5TOOLS_UTILS_H */
diff --git a/tools/lib/h5trav.h b/tools/lib/h5trav.h
index 32cd270..cda27a2 100644
--- a/tools/lib/h5trav.h
+++ b/tools/lib/h5trav.h
@@ -11,8 +11,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef H5TRAV_H__
-#define H5TRAV_H__
+#ifndef H5TRAV_H
+#define H5TRAV_H
 
 #include "hdf5.h"
 
@@ -188,4 +188,4 @@ H5TOOLS_DLL void trav_table_free(trav_table_t *table);
 
 H5TOOLS_DLL void trav_table_addflags(unsigned *flags, char *objname, h5trav_type_t type, trav_table_t *table);
 
-#endif /* H5TRAV_H__ */
+#endif /* H5TRAV_H */
diff --git a/tools/lib/io_timer.h b/tools/lib/io_timer.h
index 96ea05e..0269b93 100644
--- a/tools/lib/io_timer.h
+++ b/tools/lib/io_timer.h
@@ -11,8 +11,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef IO_TIMER__
-#define IO_TIMER__
+#ifndef IO_TIMER
+#define IO_TIMER
 
 #include "hdf5.h"
 
@@ -88,4 +88,4 @@ H5TOOLS_DLL double     io_time_get(io_time_t *pt, timer_type t);
 }
 #endif /* __cplusplus */
 
-#endif /* IO_TIMER__ */
+#endif /* IO_TIMER */
diff --git a/tools/lib/ph5diff.h b/tools/lib/ph5diff.h
index 8e884dd..7dce495 100644
--- a/tools/lib/ph5diff.h
+++ b/tools/lib/ph5diff.h
@@ -11,8 +11,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef _PH5DIFF_H__
-#define _PH5DIFF_H__
+#ifndef PH5DIFF_H
+#define PH5DIFF_H
 
 /* Send from manager to workers */
 #define MPI_TAG_ARGS      1
@@ -40,4 +40,4 @@ struct diffs_found {
     int     not_cmp;
 };
 
-#endif /* _PH5DIFF_H__ */
+#endif /* PH5DIFF_H */