[1.10 Merge] Hdf5 1 10 warnings merge (#1754)

* Warnings fixes (#1680)

* Clean stack size warnings in sio_engine (#1687)

* Fixes stack size warnings in tcoords.c (#1688)

* Address some warnings from casting away of const (#1684)

* Fixes stack size warnings in dtransform (#1696)

* Fixes stack size warnings in set_extent test (#1698)

* Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706)

* Avoid a signed overflow: check the range of `entry_ptr->age` before
increasing it instead of increasing it and then checking the range.
This quiets a GCC warning.

* Avoid the potential for signed overflow by rewriting expressions
`MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`.
This change quiets some GCC warnings.

* Change some local variables that cannot take sensible negative values
from signed to unsigned.  This quiets GCC warnings about potential
signed overflow.

* In a handful of instances, check the range of a signed integer before
increasing/decreasing it, just in case the increase/decrease overflows.
This quiets a handful of GCC signed-overflow warnings.

* Committing clang-format changes

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

* Fix object size warnings in cache.c test (#1701)

* Fix some const cast and stack/static object size warnings (#1700)

* Fix various warnings

* Move HDfree_const to H5private.h for wider use

* Print output from all ranks in parallel tests on allocation failure

* Move const pointer freeing macro to h5test.h for now

* Fixes a bug where t_cache fails due to a string size being too small (#1720)

* Fixes a bug where t_cache fails due to a string size being too small

Recent warning reductions led to an incorrect string size being passed
to h5_fileaccess, causing the test to silently fail. In addition to
fixing the bug, the test will now fail noisily on setup failures.

* Updates the t_cache test to fail noisily on setup errors

* Fix a few Clang sanitizer warnings (#1727)

* Stop lying about H5S_t const-ness (#1209)

Hyperslabs can be reworked inside several H5S callbacks, making H5S_t
non-const in some places where it is marked const. This change switches
these incorrectly const H5S_t pointer parameters and variables to
non-const where appropriate.

* Fix a few warnings after recent H5S const-related changes (#1225)

* Adjustments for HDF5 1.10

* Hdf5 1 12 Miscellaneous warnings fixes (#1718)

* Fixes const issues in the version 2 B-trees (#1172)

The operations that were changed are fundamentally not const since the
shadow operation can modify the node structure when SWMR is in use.

* Quiets const warning in H5RS code (#1181)

* Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the (#1171)

* Avoid calling H5Ropen_object with a misaligned H5R_ref_t: copy the
raw H5R_ref_t bytes to a heap buffer that's known to have the right
alignment.

* Committing clang-format changes

* Use an automatic H5R_ref_t instead of malloc'ing one.  Go ahead and
initialize the H5R_ref_t to all-0s so that arbitrary stack content
doesn't foul things up.  Bail out with an error if `size` exceeds
`sizeof(H5R_ref_t)`.

* Committing clang-format changes

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

* Miscellaneous warnings fixes

Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix several warnings (#747)

Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

4 files changed, 71 insertions, 28 deletions

diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index c465b7a..c10381d 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -1391,6 +1391,9 @@ character_compare_opt(unsigned char *mem1, unsigned char *mem2, hsize_t elemtno,
     hbool_t       both_zero = FALSE;
     double        per;
 
+    /* both_zero is set in the PER_UNSIGN macro but not used in this function */
+    (void)both_zero;
+
     HDmemcpy(&temp1_uchar, mem1, sizeof(unsigned char));
     HDmemcpy(&temp2_uchar, mem2, sizeof(unsigned char));
     H5TOOLS_START_DEBUG(" %d=%d", temp1_uchar, temp2_uchar);
diff --git a/tools/src/h5diff/ph5diff_main.c b/tools/src/h5diff/ph5diff_main.c
index 8e5c3e8..75fb9a4 100644
--- a/tools/src/h5diff/ph5diff_main.c
+++ b/tools/src/h5diff/ph5diff_main.c
@@ -312,5 +312,5 @@ h5diff_exit(int status)
     /* Always exit(0), since MPI implementations do weird stuff when they
      *  receive a non-zero exit value. - QAK
      */
-    HDexit(0);
+    HDexit(status);
 }
diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c
index ec14fdc..74bd224 100644
--- a/tools/src/h5dump/h5dump_xml.c
+++ b/tools/src/h5dump/h5dump_xml.c
@@ -2354,14 +2354,21 @@ xml_dump_named_datatype(hid_t type, const char *name)
     h5tools_context_t ctx;          /* print context  */
     h5tool_format_t * outputformat = &xml_dataformat;
     h5tool_format_t   string_dataformat;
-    char *            tmp;
-    char *            dtxid;
-    char *            parentxid;
-    char *            t_tmp;
-    char *            t_prefix;
-    char *            t_name;
+    char *            tmp       = NULL;
+    char *            dtxid     = NULL;
+    char *            parentxid = NULL;
+    char *            t_tmp     = NULL;
+    char *            t_prefix  = NULL;
+    char *            t_name    = NULL;
 
     tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
+    if (tmp == NULL) {
+        indentation(dump_indent);
+        error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
+    }
+
     HDstrcpy(tmp, prefix);
     HDstrcat(tmp, "/");
     HDstrcat(tmp, name);
@@ -2616,6 +2623,13 @@ xml_dump_group(hid_t gid, const char *name)
     }
     else {
         tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
+        if (tmp == NULL) {
+            indentation(dump_indent);
+            error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__);
+            h5tools_setstatus(EXIT_FAILURE);
+            return;
+        }
+
         HDstrcpy(tmp, prefix);
         par = HDstrdup(tmp);
         cp  = HDstrrchr(par, '/');
@@ -3126,8 +3140,11 @@ xml_print_strs(hid_t did, int source)
     }
 
     bp = (char *)buf;
-    if (!is_vlstr)
+    if (!is_vlstr) {
         onestring = (char *)HDcalloc(tsiz, sizeof(char));
+        if (onestring == NULL)
+            goto error;
+    }
 
     /* setup */
     HDmemset(&buffer, 0, sizeof(h5tools_str_t));
@@ -3749,6 +3766,14 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED *ss
     char *pstr = (char *)HDmalloc((size_t)100);
 
     tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
+    if (tmp == NULL) {
+        error_msg("buffer allocation failed\n");
+        h5tools_setstatus(EXIT_FAILURE);
+        HDfree(rstr);
+        HDfree(pstr);
+        return;
+    }
+
     HDstrcpy(tmp, prefix);
     HDstrcat(tmp, "/");
     HDstrcat(tmp, name);
diff --git a/tools/src/h5perf/sio_engine.c b/tools/src/h5perf/sio_engine.c
index dc2c68e..449e857 100644
--- a/tools/src/h5perf/sio_engine.c
+++ b/tools/src/h5perf/sio_engine.c
@@ -125,7 +125,6 @@ static hid_t    h5dxpl          = H5I_INVALID_HID; /* Dataset transfer property
  * Purpose:         SIO Engine where IO are executed.
  * Return:          results
  * Programmer:      Christian Chilan, April, 2008
- * Modifications:
  */
 void
 do_sio(parameters param, results *res)
@@ -136,18 +135,20 @@ do_sio(parameters param, results *res)
     iotype     iot;                /* API type */
     char       base_name[256];     /* test file base name */
     /* return codes */
-    herr_t ret_code = 0; /*return code                           */
+    herr_t ret_code = 0; /* return code */
 
-    char fname[FILENAME_MAX]; /* test file name */
-    int  i;
-    /* HDF5 variables */
-    herr_t hrc; /*HDF5 return code              */
+    char *fname = NULL;
+    int   i;
 
-    /* Sanity check parameters */
+    /* HDF5 variables */
+    herr_t hrc; /* HDF5 return code */
 
     /* IO type */
     iot = param.io_type;
 
+    if (NULL == (fname = HDcalloc(FILENAME_MAX, sizeof(char))))
+        GOTOERROR(FAIL);
+
     switch (iot) {
         case POSIXIO:
             fd.posixfd  = -1;
@@ -269,8 +270,8 @@ done:
     }
 
     /* release generic resources */
-    if (buffer)
-        free(buffer);
+    HDfree(buffer);
+    HDfree(fname);
 
     res->ret_code = ret_code;
 }
@@ -1127,7 +1128,6 @@ done:
  * Purpose:     Sets file driver.
  * Return:      SUCCESS or FAIL
  * Programmer:  Christian Chilan, April, 2008
- * Modifications:
  */
 
 hid_t
@@ -1166,9 +1166,11 @@ set_vfd(parameters *param)
         H5FD_mem_t  memb_map[H5FD_MEM_NTYPES];
         hid_t       memb_fapl[H5FD_MEM_NTYPES];
         const char *memb_name[H5FD_MEM_NTYPES];
-        char        sv[H5FD_MEM_NTYPES][1024];
         haddr_t     memb_addr[H5FD_MEM_NTYPES];
         H5FD_mem_t  mt;
+        struct {
+            char arr[H5FD_MEM_NTYPES][1024];
+        } *sv = NULL;
 
         HDmemset(memb_map, 0, sizeof memb_map);
         HDmemset(memb_fapl, 0, sizeof memb_fapl);
@@ -1176,16 +1178,22 @@ set_vfd(parameters *param)
         HDmemset(memb_addr, 0, sizeof memb_addr);
 
         HDassert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES);
+
+        if (NULL == (sv = HDcalloc(1, sizeof(*sv))))
+            return -1;
         for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++) {
             memb_fapl[mt] = H5P_DEFAULT;
-            HDsprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]);
-            memb_name[mt] = sv[mt];
+            HDsprintf(sv->arr[mt], "%%s-%c.h5", multi_letters[mt]);
+            memb_name[mt] = sv->arr[mt];
             memb_addr[mt] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10);
         }
 
         if (H5Pset_fapl_multi(my_fapl, memb_map, memb_fapl, memb_name, memb_addr, FALSE) < 0) {
+            HDfree(sv);
             return -1;
         }
+
+        HDfree(sv);
     }
     else if (vfd == family) {
         hsize_t fam_size = 1 * 1024 * 1024; /*100 MB*/
@@ -1264,14 +1272,18 @@ done:
  * Purpose:     Cleanup temporary file unless HDF5_NOCLEANUP is set.
  * Return:      void
  * Programmer:  Albert Cheng 2001/12/12
- * Modifications: Support for file drivers. Christian Chilan, April, 2008
  */
 static void
 do_cleanupfile(iotype iot, char *filename)
 {
-    char  temp[2048];
-    int   j;
-    hid_t driver;
+    char * temp = NULL;
+    size_t temp_sz;
+    int    j;
+    hid_t  driver;
+
+    temp_sz = (2048) * sizeof(char);
+    if (NULL == (temp = HDcalloc(1, temp_sz)))
+        goto done;
 
     if (clean_file_g == -1)
         clean_file_g = (HDgetenv("HDF5_NOCLEANUP") == NULL) ? 1 : 0;
@@ -1288,7 +1300,7 @@ do_cleanupfile(iotype iot, char *filename)
 
                 if (driver == H5FD_FAMILY) {
                     for (j = 0; /*void*/; j++) {
-                        HDsnprintf(temp, sizeof temp, filename, j);
+                        HDsnprintf(temp, temp_sz, filename, j);
 
                         if (HDaccess(temp, F_OK) < 0)
                             break;
@@ -1307,10 +1319,10 @@ do_cleanupfile(iotype iot, char *filename)
                 }
                 else if (driver == H5FD_MULTI) {
                     H5FD_mem_t mt;
-                    assert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES);
+                    HDassert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES);
 
                     for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++) {
-                        HDsnprintf(temp, sizeof temp, "%s-%c.h5", filename, multi_letters[mt]);
+                        HDsnprintf(temp, temp_sz, "%s-%c.h5", filename, multi_letters[mt]);
                         HDremove(temp); /*don't care if it fails*/
                     }
                 }
@@ -1327,4 +1339,7 @@ do_cleanupfile(iotype iot, char *filename)
                 break;
         }
     }
+
+done:
+    HDfree(temp);
 }