Sync 1.14 branch with develop (#3705)

* Address nagfor exceptions stoppage. (#3658)

* added cmake ieee flag for nagfor

* generalized determining the nag compiler

* fixing some misc. NAG warnings

* Simplify. (#3659)


* Address @jhendersonHDF review

* Add expedited testing support to t_filters_parallel (#3665)

* Remove clang warnings (#3656)

* Fixes test failure for gfortran -O2 and -O3, -fdefault-real-16 (#3662)

* added cmake ieee flag for nagfor

* fixes gfortran -O2 and -O3, -fdefault-real-16

* fixed sync

* updated release notes

* Fix link error on clang17/gfortran13/macOS-13 (#3666) (#3671)

* Correct fortran CMake generator expressions (#3670)

* Add AOCC GitHub Action (#3504) (#3657)

* Fix uninitialized subfiling test variable (#3675)

Picked up by gcc 10 on skybridge. Probably spurious, but no harm in
initializing it to a "bad" value.

* Add support for AOCC & Flang w/ the Autotools (#3674)

* Adds a config/clang-fflags options file to support Flang
* Corrects missing "-Wl," from linker options in the libtool wrappers
  when using Flang, the MPI Fortran compiler wrappers, and building
  the shared library. This would often result in unrecognized options
  like -soname.
* Enable -nomp w/ Flang to avoid linking to the OpenMPI library.

CMake can build the parallel, shared library w/ Fortran using AOCC
and Flang, so no changes were needed for that build system.

Fixes GitHub issues #3439, #1588, #366, #280

* Fix a strncpy call to use dest size not src (#3677)

A strncpy call in a path construction call used the size of the src
buffer instead of the dest buffer as the limit n.

This was switched to use the dest size and properly terminate the
string if truncation occurs.

* Remove CANBE_UNUSED() from subfiling VFD (#3678)

This macro was an attempt to quiet warnings about release mode unused
variables that only appear in asserts. It resolves to a void cast, which
doesn't quiet warnings when an assignment has already taken place.

* Suppress MPI_Waitall warnings w/ MPICH (#3680)

MPICH defines MPI_STATUSES_IGNORE (a pointer) to 1, which raises warnings
w/ gcc. This is a known issue that the MPICH devs are not going to fix.

See here:
    https://github.com/pmodels/mpich/issues/5687

This fix suppresses those issues w/ gcc

* Fix a possible NULL pointer dereference in tests (#3676)


The dtypes test could dereference a NULL pointer if a strdup call
failed.

* Fix printf warnings in t_mpi (#3679)

* Fix printf warnings in t_mpi

The type of MPI_Offset varies with implementation. In MPICH, it's long,
which raises warnings when we attempt to use long long format
specifiers. Casting to long long fixes the warnings.

* Fix invalid memory access in S3 comms (#3681)

In the ros3 VFD, passing an empty string parameter to an internal
API call could result in accessing the -1th element of a string.
This would cause failures on big-endian systems like s390x.

This parameter is now checked before writing to the string.

Fixes GitHub #1168

* Add Doxygen for H5Pset_fapl_sec2() (#3685)

*

* switch to using time function instead of date function (#3690)

* Initialize API context MPI types to MPI_BYTE (#3688)

* Add test info output to t_filters_parallel (#3696)

* Suppress format string warnings in subfiling test (#3699)

* Fix unused variable in tselect.c (#3701)

* Fix unused variable warning in H5F_sfile_assert_num (#3700)

* Restore floating-point suffixes in tests (#3698)

A prior commit removed too many F suffixes. This restores the suffixes
for float variables.

* Sync with changes from develop

---------

Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

10 files changed, 82 insertions, 46 deletions

diff --git a/src/H5CX.c b/src/H5CX.c
index aa9d0b5..b3b2fca 100644
--- a/src/H5CX.c
+++ b/src/H5CX.c
@@ -778,6 +778,11 @@ H5CX__push_common(H5CX_node_t *cnode)
     cnode->ctx.tag     = H5AC__INVALID_TAG;
     cnode->ctx.ring    = H5AC_RING_USER;
 
+#ifdef H5_HAVE_PARALLEL
+    cnode->ctx.btype = MPI_BYTE;
+    cnode->ctx.ftype = MPI_BYTE;
+#endif
+
     /* Push context node onto stack */
     cnode->next = *head;
     *head       = cnode;
diff --git a/src/H5FDs3comms.c b/src/H5FDs3comms.c
index 58fc435..dae1149 100644
--- a/src/H5FDs3comms.c
+++ b/src/H5FDs3comms.c
@@ -1713,7 +1713,8 @@ H5FD_s3comms_aws_canonical_request(char *canonical_request_dest, int _cr_size, c
     } /* end while node is not NULL */
 
     /* remove trailing ';' from signed headers sequence */
-    signed_headers_dest[strlen(signed_headers_dest) - 1] = '\0';
+    if (*signed_headers_dest != '\0')
+        signed_headers_dest[strlen(signed_headers_dest) - 1] = '\0';
 
     /* append signed headers and payload hash
      * NOTE: at present, no HTTP body is handled, per the nature of
diff --git a/src/H5FDsec2.h b/src/H5FDsec2.h
index 56f4575..a2590ae 100644
--- a/src/H5FDsec2.h
+++ b/src/H5FDsec2.h
@@ -23,7 +23,23 @@
 extern "C" {
 #endif
 
-H5_DLL hid_t  H5FD_sec2_init(void);
+H5_DLL hid_t H5FD_sec2_init(void);
+
+/**
+ * \ingroup FAPL
+ *
+ * \brief Modifies the file access property list to use the #H5FD_SEC2 driver
+ *
+ * \fapl_id
+ *
+ * \returns \herr_t
+ *
+ * \details H5Pset_fapl_sec2() modifies the file access property list to use the
+ *          #H5FD_SEC2 driver.
+ *
+ * \since 1.4.0
+ *
+ */
 H5_DLL herr_t H5Pset_fapl_sec2(hid_t fapl_id);
 
 #ifdef __cplusplus
diff --git a/src/H5FDsubfiling/H5FDioc.c b/src/H5FDsubfiling/H5FDioc.c
index 39766de..80771c0 100644
--- a/src/H5FDsubfiling/H5FDioc.c
+++ b/src/H5FDsubfiling/H5FDioc.c
@@ -32,8 +32,6 @@
 #include "H5MMprivate.h"  /* Memory management        */
 #include "H5Pprivate.h"   /* Property lists           */
 
-#define CANBE_UNUSED(X) (void)(X)
-
 /* The driver identification number, initialized at runtime */
 static hid_t H5FD_IOC_g = H5I_INVALID_HID;
 
@@ -1219,13 +1217,14 @@ static herr_t
 H5FD__ioc_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr,
                size_t size, void *buf)
 {
-    H5FD_ioc_t *file      = (H5FD_ioc_t *)_file;
-    herr_t      ret_value = SUCCEED;
+#ifndef NDEBUG
+    H5FD_ioc_t *file = (H5FD_ioc_t *)_file;
+#endif
+    herr_t ret_value = SUCCEED;
 
     H5FD_IOC_LOG_CALL(__func__);
 
     assert(file && file->pub.cls);
-    CANBE_UNUSED(file);
     assert(buf);
 
     /* Check for overflow conditions */
diff --git a/src/H5FDsubfiling/H5FDioc_int.c b/src/H5FDsubfiling/H5FDioc_int.c
index 674b08d..5528fc8 100644
--- a/src/H5FDsubfiling/H5FDioc_int.c
+++ b/src/H5FDsubfiling/H5FDioc_int.c
@@ -423,8 +423,14 @@ ioc__async_completion(MPI_Request *mpi_reqs, size_t num_reqs)
     assert(mpi_reqs);
 
     H5_CHECK_OVERFLOW(num_reqs, size_t, int);
+
+    /* Have to supppress gcc warnings regarding MPI_STATUSES_IGNORE
+     * with MPICH (https://github.com/pmodels/mpich/issues/5687)
+     */
+    H5_GCC_DIAG_OFF("stringop-overflow")
     if (MPI_SUCCESS != (mpi_code = MPI_Waitall((int)num_reqs, mpi_reqs, MPI_STATUSES_IGNORE)))
         H5_SUBFILING_MPI_GOTO_ERROR(FAIL, "MPI_Waitall failed", mpi_code);
+    H5_GCC_DIAG_ON("stringop-overflow")
 
 done:
     H5_SUBFILING_FUNC_LEAVE;
diff --git a/src/H5FDsubfiling/H5FDsubfile_int.c b/src/H5FDsubfiling/H5FDsubfile_int.c
index cb210b6..a7dd864 100644
--- a/src/H5FDsubfiling/H5FDsubfile_int.c
+++ b/src/H5FDsubfiling/H5FDsubfile_int.c
@@ -143,17 +143,19 @@ H5FD__subfiling__truncate_sub_files(hid_t context_id, int64_t logical_file_eof,
         }
 
         /* Wait for truncate operations to complete */
+        H5_GCC_DIAG_OFF("stringop-overflow")
         if (MPI_SUCCESS != (mpi_code = MPI_Waitall(num_subfiles_owned, recv_reqs, MPI_STATUSES_IGNORE)))
             H5_SUBFILING_MPI_GOTO_ERROR(FAIL, "MPI_Waitall", mpi_code);
-
-            /* sanity check -- compute the file eof using the same mechanism used to
-             * compute the subfile eof.  Assert that the computed value and the
-             * actual value match.
-             *
-             * Do this only for debug builds -- probably delete this before release.
-             *
-             *                                           JRM -- 12/15/21
-             */
+        H5_GCC_DIAG_ON("stringop-overflow")
+
+        /* sanity check -- compute the file eof using the same mechanism used to
+         * compute the subfile eof.  Assert that the computed value and the
+         * actual value match.
+         *
+         * Do this only for debug builds -- probably delete this before release.
+         *
+         *                                           JRM -- 12/15/21
+         */
 
 #ifndef NDEBUG
         {
@@ -339,15 +341,18 @@ H5FD__subfiling__get_real_eof(hid_t context_id, int64_t *logical_eof_ptr)
     }
 
     /* Wait for EOF communication to complete */
+    H5_GCC_DIAG_OFF("stringop-overflow")
     if (MPI_SUCCESS != (mpi_code = MPI_Waitall(num_subfiles, recv_reqs, MPI_STATUSES_IGNORE)))
         H5_SUBFILING_MPI_GOTO_ERROR(FAIL, "MPI_Waitall", mpi_code);
+    H5_GCC_DIAG_ON("stringop-overflow")
 
     for (int i = 0; i < num_subfiles; i++) {
+#ifndef NDEBUG
         int ioc_rank = (int)recv_msg[3 * i];
+#endif
 
         assert(ioc_rank >= 0);
         assert(ioc_rank < n_io_concentrators);
-        CANBE_UNUSED(ioc_rank);
         assert(sf_eofs[i] == -1);
 
         sf_eofs[i] = recv_msg[(3 * i) + 1];
diff --git a/src/H5FDsubfiling/H5FDsubfiling.c b/src/H5FDsubfiling/H5FDsubfiling.c
index d8616c8..a2daba0 100644
--- a/src/H5FDsubfiling/H5FDsubfiling.c
+++ b/src/H5FDsubfiling/H5FDsubfiling.c
@@ -1556,7 +1556,7 @@ H5FD__subfiling_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_i
         H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined, addr = %" PRIuHADDR, addr);
     if (REGION_OVERFLOW(addr, size))
         H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL,
-                                "addr overflow, addr = %" PRIuHADDR ", size = %" PRIuHADDR, addr, size);
+                                "addr overflow, addr = %" PRIuHADDR ", size = %zu", addr, size);
 
     /* Temporarily reject collective I/O until support is implemented (unless types are simple MPI_BYTE) */
     {
@@ -1789,7 +1789,7 @@ H5FD__subfiling_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_
         H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined, addr = %" PRIuHADDR, addr);
     if (REGION_OVERFLOW(addr, size))
         H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL,
-                                "addr overflow, addr = %" PRIuHADDR ", size = %" PRIuHADDR, addr, size);
+                                "addr overflow, addr = %" PRIuHADDR ", size = %zu", addr, size);
 
     /* Temporarily reject collective I/O until support is implemented (unless types are simple MPI_BYTE) */
     {
diff --git a/src/H5FDsubfiling/H5FDsubfiling_priv.h b/src/H5FDsubfiling/H5FDsubfiling_priv.h
index 9cc32f1..08fef7d 100644
--- a/src/H5FDsubfiling/H5FDsubfiling_priv.h
+++ b/src/H5FDsubfiling/H5FDsubfiling_priv.h
@@ -63,6 +63,4 @@ H5_DLL herr_t H5FD__subfiling__get_real_eof(hid_t context_id, int64_t *logical_e
 }
 #endif
 
-#define CANBE_UNUSED(X) (void)(X)
-
 #endif /* H5FDsubfiling_priv_H */
diff --git a/src/H5Fsfile.c b/src/H5Fsfile.c
index ef80a79..6cf2c80 100644
--- a/src/H5Fsfile.c
+++ b/src/H5Fsfile.c
@@ -47,14 +47,17 @@ static H5F_sfile_node_t *H5F_sfile_head_s = NULL;
  *-------------------------------------------------------------------------
  */
 void
-H5F_sfile_assert_num(unsigned n)
+H5F_sfile_assert_num(unsigned H5_ATTR_NDEBUG_UNUSED n)
 {
     FUNC_ENTER_NOAPI_NOINIT_NOERR
 
+    /* The only useful work this function does is asserting so when NDEBUG
+     * is defined it's a no-op.
+     */
+#ifndef NDEBUG
     if (n == 0) {
-        /* Sanity checking */
         assert(H5F_sfile_head_s == NULL);
-    } /* end if */
+    }
     else {
         unsigned          count; /* Number of open shared files */
         H5F_sfile_node_t *curr;  /* Current shared file node */
@@ -68,11 +71,11 @@ H5F_sfile_assert_num(unsigned n)
 
             /* Advance to next shared file node */
             curr = curr->next;
-        } /* end while */
+        }
 
-        /* Sanity checking */
         assert(count == n);
-    } /* end else */
+    }
+#endif
 
     FUNC_LEAVE_NOAPI_VOID
 } /* H5F_sfile_assert_num() */
diff --git a/src/H5system.c b/src/H5system.c
index 7ff521e..30a89a1 100644
--- a/src/H5system.c
+++ b/src/H5system.c
@@ -620,7 +620,6 @@ H5_build_extpath(const char *name, char **extpath /*out*/)
 
     FUNC_ENTER_NOAPI_NOINIT
 
-    /* Sanity check */
     assert(name);
     assert(extpath);
 
@@ -634,8 +633,9 @@ H5_build_extpath(const char *name, char **extpath /*out*/)
     if (H5_CHECK_ABSOLUTE(name)) {
         if (NULL == (full_path = (char *)H5MM_strdup(name)))
             HGOTO_ERROR(H5E_INTERNAL, H5E_NOSPACE, FAIL, "memory allocation failed");
-    }      /* end if */
-    else { /* relative pathname */
+    }
+    else {
+        /* relative pathname */
         char  *retcwd;
         size_t name_len;
         int    drive;
@@ -655,12 +655,12 @@ H5_build_extpath(const char *name, char **extpath /*out*/)
             drive  = HDtoupper(name[0]) - 'A' + 1;
             retcwd = HDgetdcwd(drive, cwdpath, MAX_PATH_LEN);
             strncpy(new_name, &name[2], name_len);
-        } /* end if */
-          /*
-           * Windows: name[0] is a '/' or '\'
-           *  Get current drive
-           * Unix: does not apply
-           */
+        }
+        /*
+         * Windows: name[0] is a '/' or '\'
+         *  Get current drive
+         * Unix: does not apply
+         */
         else if (H5_CHECK_ABS_PATH(name) && (0 != (drive = HDgetdrive()))) {
             snprintf(cwdpath, MAX_PATH_LEN, "%c:%c", (drive + 'A' - 1), name[0]);
             retcwd = cwdpath;
@@ -670,28 +670,32 @@ H5_build_extpath(const char *name, char **extpath /*out*/)
         else {
             retcwd = HDgetcwd(cwdpath, MAX_PATH_LEN);
             strncpy(new_name, name, name_len);
-        } /* end if */
+        }
 
         if (retcwd != NULL) {
             size_t cwdlen;
             size_t path_len;
 
-            assert(cwdpath);
             cwdlen = strlen(cwdpath);
-            assert(cwdlen);
-            assert(new_name);
+            if (cwdlen == 0)
+                HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "cwd length is zero");
             path_len = cwdlen + strlen(new_name) + 2;
             if (NULL == (full_path = (char *)H5MM_malloc(path_len)))
                 HGOTO_ERROR(H5E_INTERNAL, H5E_NOSPACE, FAIL, "memory allocation failed");
 
-            strncpy(full_path, cwdpath, cwdlen + 1);
+            /* path_len will always be greater than zero, so no check before
+             * setting the terminal NUL byte of full_path
+             */
+            strncpy(full_path, cwdpath, path_len);
+            full_path[path_len - 1] = '\0';
+
             if (!H5_CHECK_DELIMITER(cwdpath[cwdlen - 1]))
                 strncat(full_path, H5_DIR_SEPS, path_len - (cwdlen + 1));
             strncat(full_path, new_name, path_len - (cwdlen + 1) - strlen(H5_DIR_SEPS));
-        } /* end if */
-    }     /* end else */
+        }
+    }
 
-    /* strip out the last component (the file name itself) from the path */
+    /* Strip out the last component (the file name itself) from the path */
     if (full_path) {
         char *ptr = NULL;
 
@@ -699,10 +703,9 @@ H5_build_extpath(const char *name, char **extpath /*out*/)
         assert(ptr);
         *++ptr   = '\0';
         *extpath = full_path;
-    } /* end if */
+    }
 
 done:
-    /* Release resources */
     if (cwdpath)
         H5MM_xfree(cwdpath);
     if (new_name)