Cherry-pick 12 develop branch PRs to hdf5_1_12 (#622)

* Snapshot version 1.12 release 1-3.  Update  version to 1.12.1-4.

* First cut of the H5 public API documentation. (#80)

* First cut of the H5 public API documentation.

* Added H5Z "bonus track."

* Applied Quincey's patch.

* Added the missing patches from Quincey's original patch.

* H5PL (complete) and basic H5VL API documentation.

* Added H5I API docs.

* Added H5L API docs.

* First installment from Elena's H5T batch.

* Second installment of Elena's H5T batch.

* Final installment of Elena's H5T batch.

* Full set of current H5F documentation. (#105)

* First cut of the H5 public API documentation.

* Added H5Z "bonus track."

* Applied Quincey's patch.

* Added the missing patches from Quincey's original patch.

* H5PL (complete) and basic H5VL API documentation.

* Added H5I API docs.

* Added H5L API docs.

* First installment from Elena's H5T batch.

* Second installment of Elena's H5T batch.

* Final installment of Elena's H5T batch.

* Migrated documentation for SWMR functions.

* Catching up on MDC functions.

* Integrated the H5F MDC function documentation.

* Added MDC and parallel H5F functions.

* Slightly updated main page.

* Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.

* Doxygen - added (mostly) beginner functions (#112)

* Doxygen - added (mostly) beginner functions

* Removed duplicate H5Pset_szip function

* Add src/H5module.h to MANIFEST.

* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer.   Update test to be more thorough with using compound datatype fields everywhere. (#206)

* Modify temporary rpath for testing in java example scripts. (#230)

* Fix undefined left shifting of negative numbers (#338)

Undefined Bahavior Sanitizer errored here about left shifting negative numbers.

* Fixes various warnings noticed on Windows (#425)

* Fixes various warnings noticed on Windows

- Adds a prototype for our implementation of vasprintf
- Return type of H5_get_utf16_str() is now non-const
- Fixes possible uninitialized return type in Wremove_utf8
- Better isolation of fork() code in accum.c:test_swmr_write_big()
- Better isolation of non-zlib code in dsets.c:test_filter_delete()
- Removed unused variable in trefer.c:test_reference_cmpnd_obj()

* Fixes clang-format issues

* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)

* Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes

Removes useless const declarations.

* Fixed most readability-non-const-parameter warnings

These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature.

* Reformat source with clang v10.0.1.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Added C++11 override keyword where appropriate (#433)

Added H5_OVERRIDE macro for compatibility with both C++11 and older.

* Various clang tidy warning fixes (#448)

* Fixed clang-tidy bugprone-reserved-identifier warnings

* Fixed clang-tidy bugprone-assert-side-effect warnings

* Fixed clang-tidy bugprone-copy-constructor-init warning

* Fixed clang-tidy readability-redundant-preprocessor warning

For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block.

Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing.  Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS.

* Fixed clang-tidy readability-redundant-string-init warnings

* Fixed some clang-tidy performance-type-promotion-in-math-fn warnings

* Fixed clang-tidy performance-unnecessary-value-param warnings

* Reformat source with clang v10.0.1.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Removed checks/workarounds for pre-C++89 compatibility (#449)

After 30+ years, just assume that the following exist:
- extension-less includes
- namespaces
- std::
- static_cast
- bool

* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)

* Fixed all clang-tidy bugprone-suspicious-string-compare warnings

This change was generated entirely by clang-tidy itself.

* Reformat code with clang v10.0.1.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.

* Minor parallel improvements (#519)

* Improve MPI error reporting, handled failed operations in parallel tests more nicely, and clean up MPI_Allreduce for determining whether to break collective I/O

* Committing clang-format changes

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

* Clean up MPI-IO VFD tracing support (#520)

* Clean up tracing support

* Committing clang-format changes

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

* Brings the native implementation of H5Fdelete() from Bitbucket (#524)

* Committing clang-format changes

* Brings the native VFD H5Fdelete() implementation from Bitbucket

Only brings the 'del' callbacks, not the 'open/close' scheme.

* Formatter changes

* Committing clang-format changes

* Fixes direct VFD callback name

* Removes UNUSED macro from family API call

* Adds barrier and rank 0 check to MPI-I/O VFD delete

* Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete"

This reverts commit 909765f759d9d96e84f4b8b1cc14f7d2b3ac8143.

* Revert "Revert "Adds barrier and rank 0 check to MPI-I/O VFD delete""

This reverts commit 9b04bef1157853fc79fcb8fcc3e8ba1371091702.

* Adds a second barrier after the delete in MPI-I/O VFD

* Only delete files in the core VFD when the backing store flag is set

* Fixes string issues in multi VFD

Also, h5test.c cleanup code now uses H5Fdelete().

* Formatted source

* Rework fapl checks for MPI-I/O VFD delete callback

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

* Minor warning fixes in develop (#526)

* Committing clang-format changes

* Minor warning fixes

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

* Removes implementation of my_strdup() from the multi VFD (#527)

* Committing clang-format changes

* Removes my_strdup() from the multi VFD

* Use strdup directly when memory sanity checks are off

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

* Removes dead H5ST package from the library (#528)

* Committing clang-format changes

* Removes the unused H5ST package from the library

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

* Fix HDFFV-11232 (#530)

* fixed missed closing of a dataset

* fixed missed closing of a dataset

* fixed typo in error return

* Committing clang-format changes

* minor edits

* code format

* Committing clang-format changes

* code format

* minor edit

* added H5fortkit dependency for H5VLff.F90, HDFFV-11232

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

* Fixes incorrect usage of H5I_BADID (#554)

* Committing clang-format changes

* Fixes incorrect use of H5I_BADID

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

* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601)

* Committing clang-format changes

* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times

An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.

Fixes HDFFV-11239

* Fixes typos

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

* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)

* Committing clang-format changes

* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID

This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.

This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.

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

* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)

* Committing clang-format changes

* Fixes incorrect size_hint handling in H5Gcreate1

* Updates the size hint type for group creation

* Updates the RELEASE.txt note

* Revert "Updates the RELEASE.txt note"

This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff.

* Reverts previous behavior to use a uint32_t struct field

* Updates RELEASE.txt

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

* Revert "Brings the native implementation of H5Fdelete() from Bitbucket (#524)"

This reverts commit 38d1b121ae428138b8863c2a319518c7363c2d94.

Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>

1 files changed, 122 insertions, 114 deletions

diff --git a/src/H5FDlog.c b/src/H5FDlog.c
index aa2d6db..7214b75 100644
--- a/src/H5FDlog.c
+++ b/src/H5FDlog.c
@@ -326,12 +326,15 @@ H5Pset_fapl_log(hid_t fapl_id, const char *logfile, unsigned long long flags, si
     FUNC_ENTER_API(FAIL)
     H5TRACE4("e", "i*sULz", fapl_id, logfile, flags, buf_size);
 
+    /* Do this first, so that we don't try to free a wild pointer if
+     * H5P_object_verify() fails.
+     */
+    HDmemset(&fa, 0, sizeof(H5FD_log_fapl_t));
+
     /* Check arguments */
     if (NULL == (plist = H5P_object_verify(fapl_id, H5P_FILE_ACCESS)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access property list")
 
-    HDmemset(&fa, 0, sizeof(H5FD_log_fapl_t));
-
     /* Duplicate the log file string
      * A little wasteful, since this string will just be copied later, but
      * passing it in as a pointer sets off a chain of impossible-to-resolve
@@ -426,7 +429,7 @@ done:
             if (new_fa->logfile)
                 new_fa->logfile = (char *)H5MM_xfree(new_fa->logfile);
             H5MM_free(new_fa);
-        } /* end if */
+        }
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5FD__log_fapl_copy() */
@@ -484,8 +487,8 @@ H5FD__log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
 #ifdef H5_HAVE_WIN32_API
     struct _BY_HANDLE_FILE_INFORMATION fileinfo;
 #endif
-    H5_timer_t open_timer = {{0}, {0}, {0}, FALSE}; /* Timer for open() call */
-    H5_timer_t stat_timer = {{0}, {0}, {0}, FALSE}; /* Timer for stat() call */
+    H5_timer_t open_timer; /* Timer for open() call */
+    H5_timer_t stat_timer; /* Timer for stat() call */
     h5_stat_t  sb;
     H5FD_t *   ret_value = NULL; /* Return value */
 
@@ -502,6 +505,10 @@ H5FD__log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
     if (ADDR_OVERFLOW(maxaddr))
         HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, NULL, "bogus maxaddr")
 
+    /* Initialize timers */
+    H5_timer_init(&open_timer);
+    H5_timer_init(&stat_timer);
+
     /* Build the open flags */
     o_flags = (H5F_ACC_RDWR & flags) ? O_RDWR : O_RDONLY;
     if (H5F_ACC_TRUNC & flags)
@@ -518,10 +525,8 @@ H5FD__log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
         HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, NULL, "bad VFL driver info")
 
     /* Start timer for open() call */
-    if (fa->flags & H5FD_LOG_TIME_OPEN) {
-        H5_timer_init(&open_timer);
+    if (fa->flags & H5FD_LOG_TIME_OPEN)
         H5_timer_start(&open_timer);
-    } /* end if */
 
     /* Open the file */
     if ((fd = HDopen(name, o_flags, H5_POSIX_CREATE_MODE_RW)) < 0) {
@@ -531,17 +536,15 @@ H5FD__log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
             H5E_FILE, H5E_CANTOPENFILE, NULL,
             "unable to open file: name = '%s', errno = %d, error message = '%s', flags = %x, o_flags = %x",
             name, myerrno, HDstrerror(myerrno), flags, (unsigned)o_flags);
-    } /* end if */
+    }
 
     /* Stop timer for open() call */
     if (fa->flags & H5FD_LOG_TIME_OPEN)
         H5_timer_stop(&open_timer);
 
     /* Start timer for stat() call */
-    if (fa->flags & H5FD_LOG_TIME_STAT) {
-        H5_timer_init(&stat_timer);
+    if (fa->flags & H5FD_LOG_TIME_STAT)
         H5_timer_start(&stat_timer);
-    } /* end if */
 
     /* Get the file stats */
     if (HDfstat(fd, &sb) < 0)
@@ -594,15 +597,15 @@ H5FD__log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
         if (file->fa.flags & H5FD_LOG_FILE_READ) {
             file->nread = (unsigned char *)H5MM_calloc(file->iosize);
             HDassert(file->nread);
-        } /* end if */
+        }
         if (file->fa.flags & H5FD_LOG_FILE_WRITE) {
             file->nwrite = (unsigned char *)H5MM_calloc(file->iosize);
             HDassert(file->nwrite);
-        } /* end if */
+        }
         if (file->fa.flags & H5FD_LOG_FLAVOR) {
             file->flavor = (unsigned char *)H5MM_calloc(file->iosize);
             HDassert(file->flavor);
-        } /* end if */
+        }
 
         /* Set the log file pointer */
         if (fa->logfile)
@@ -616,14 +619,14 @@ H5FD__log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
 
             H5_timer_get_times(open_timer, &open_times);
             HDfprintf(file->logfp, "Open took: (%f s)\n", open_times.elapsed);
-        } /* end if */
+        }
         if (file->fa.flags & H5FD_LOG_TIME_STAT) {
             H5_timevals_t stat_times; /* Elapsed time for stat() call */
 
             H5_timer_get_times(stat_timer, &stat_times);
             HDfprintf(file->logfp, "Stat took: (%f s)\n", stat_times.elapsed);
-        } /* end if */
-    }     /* end if */
+        }
+    }
 
     /* Check the file locking flags in the fapl */
     if (ignore_disabled_file_locks_s != FAIL)
@@ -645,7 +648,7 @@ H5FD__log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
         if (H5P_exist_plist(plist, H5F_ACS_FAMILY_TO_SINGLE_NAME) > 0)
             if (H5P_get(plist, H5F_ACS_FAMILY_TO_SINGLE_NAME, &file->fam_to_single) < 0)
                 HGOTO_ERROR(H5E_VFL, H5E_CANTGET, NULL, "can't get property of changing family to single")
-    } /* end if */
+    }
 
     /* Set return value */
     ret_value = (H5FD_t *)file;
@@ -656,7 +659,7 @@ done:
             HDclose(fd);
         if (file)
             file = H5FL_FREE(H5FD_log_t, file);
-    } /* end if */
+    }
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5FD__log_open() */
@@ -677,20 +680,21 @@ done:
 static herr_t
 H5FD__log_close(H5FD_t *_file)
 {
-    H5FD_log_t *file        = (H5FD_log_t *)_file;
-    H5_timer_t  close_timer = {{0}, {0}, {0}, FALSE}; /* Timer for close() call */
-    herr_t      ret_value   = SUCCEED;                /* Return value */
+    H5FD_log_t *file = (H5FD_log_t *)_file;
+    H5_timer_t  close_timer;         /* Timer for close() call */
+    herr_t      ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_STATIC
 
     /* Sanity check */
     HDassert(file);
 
+    /* Initialize timer */
+    H5_timer_init(&close_timer);
+
     /* Start timer for close() call */
-    if (file->fa.flags & H5FD_LOG_TIME_CLOSE) {
-        H5_timer_init(&close_timer);
+    if (file->fa.flags & H5FD_LOG_TIME_CLOSE)
         H5_timer_start(&close_timer);
-    } /* end if */
 
     /* Close the underlying file */
     if (HDclose(file->fd) < 0)
@@ -711,7 +715,7 @@ H5FD__log_close(H5FD_t *_file)
 
             H5_timer_get_times(close_timer, &close_times);
             HDfprintf(file->logfp, "Close took: (%f s)\n", close_times.elapsed);
-        } /* end if */
+        }
 
         /* Dump the total number of seek/read/write operations */
         if (file->fa.flags & H5FD_LOG_NUM_READ)
@@ -746,13 +750,13 @@ H5FD__log_close(H5FD_t *_file)
                               last_addr, (addr - 1), (unsigned long)(addr - last_addr), (int)last_val);
                     last_val  = file->nwrite[addr];
                     last_addr = addr;
-                } /* end if */
+                }
                 addr++;
-            } /* end while */
+            }
             HDfprintf(file->logfp,
                       "\tAddr %10" PRIuHADDR "-%10" PRIuHADDR " (%10lu bytes) written to %3d times\n",
                       last_addr, (addr - 1), (unsigned long)(addr - last_addr), (int)last_val);
-        } /* end if */
+        }
 
         /* Dump the read I/O information */
         if (file->fa.flags & H5FD_LOG_FILE_READ) {
@@ -767,13 +771,13 @@ H5FD__log_close(H5FD_t *_file)
                               last_addr, (addr - 1), (unsigned long)(addr - last_addr), (int)last_val);
                     last_val  = file->nread[addr];
                     last_addr = addr;
-                } /* end if */
+                }
                 addr++;
-            } /* end while */
+            }
             HDfprintf(file->logfp,
                       "\tAddr %10" PRIuHADDR "-%10" PRIuHADDR " (%10lu bytes) read from %3d times\n",
                       last_addr, (addr - 1), (unsigned long)(addr - last_addr), (int)last_val);
-        } /* end if */
+        }
 
         /* Dump the I/O flavor information */
         if (file->fa.flags & H5FD_LOG_FLAVOR) {
@@ -788,12 +792,12 @@ H5FD__log_close(H5FD_t *_file)
                               last_addr, (addr - 1), (unsigned long)(addr - last_addr), flavors[last_val]);
                     last_val  = file->flavor[addr];
                     last_addr = addr;
-                } /* end if */
+                }
                 addr++;
-            } /* end while */
+            }
             HDfprintf(file->logfp, "\tAddr %10" PRIuHADDR "-%10" PRIuHADDR " (%10lu bytes) flavor is %s\n",
                       last_addr, (addr - 1), (unsigned long)(addr - last_addr), flavors[last_val]);
-        } /* end if */
+        }
 
         /* Free the logging information */
         if (file->fa.flags & H5FD_LOG_FILE_WRITE)
@@ -920,7 +924,7 @@ H5FD__log_query(const H5FD_t *_file, unsigned long *flags /* out */)
         if (file && file->fam_to_single)
             *flags |= H5FD_FEAT_IGNORE_DRVRINFO; /* Ignore the driver info when file is opened (which
                                                     eliminates it) */
-    }                                            /* end if */
+    }
 
     FUNC_LEAVE_NOAPI(SUCCEED)
 } /* end H5FD__log_query() */
@@ -959,13 +963,13 @@ H5FD__log_alloc(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hs
             HDassert(addr < file->iosize);
             H5_CHECK_OVERFLOW(size, hsize_t, size_t);
             HDmemset(&file->flavor[addr], (int)type, (size_t)size);
-        } /* end if */
+        }
 
         if (file->fa.flags & H5FD_LOG_ALLOC)
             HDfprintf(file->logfp,
                       "%10" PRIuHADDR "-%10" PRIuHADDR " (%10" PRIuHSIZE " bytes) (%s) Allocated\n", addr,
                       (haddr_t)((addr + size) - 1), size, flavors[type]);
-    } /* end if */
+    }
 
     /* Set return value */
     ret_value = addr;
@@ -998,13 +1002,13 @@ H5FD__log_free(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
             HDassert(addr < file->iosize);
             H5_CHECK_OVERFLOW(size, hsize_t, size_t);
             HDmemset(&file->flavor[addr], H5FD_MEM_DEFAULT, (size_t)size);
-        } /* end if */
+        }
 
         /* Log the file memory freed */
         if (file->fa.flags & H5FD_LOG_FREE)
             HDfprintf(file->logfp, "%10" PRIuHADDR "-%10" PRIuHADDR " (%10" PRIuHSIZE " bytes) (%s) Freed\n",
                       addr, (haddr_t)((addr + size) - 1), size, flavors[type]);
-    } /* end if */
+    }
 
     FUNC_LEAVE_NOAPI(SUCCEED)
 } /* end H5FD__log_free() */
@@ -1065,14 +1069,14 @@ H5FD__log_set_eoa(H5FD_t *_file, H5FD_mem_t type, haddr_t addr)
                 HDassert(addr < file->iosize);
                 H5_CHECK_OVERFLOW(size, hsize_t, size_t);
                 HDmemset(&file->flavor[file->eoa], (int)type, (size_t)size);
-            } /* end if */
+            }
 
             /* Log the extension like an allocation */
             if (file->fa.flags & H5FD_LOG_ALLOC)
                 HDfprintf(file->logfp,
                           "%10" PRIuHADDR "-%10" PRIuHADDR " (%10" PRIuHSIZE " bytes) (%s) Allocated\n",
                           file->eoa, addr, size, flavors[type]);
-        } /* end if */
+        }
 
         /* Check for decreasing file size */
         if (H5F_addr_lt(addr, file->eoa) && H5F_addr_gt(addr, 0)) {
@@ -1083,15 +1087,15 @@ H5FD__log_set_eoa(H5FD_t *_file, H5FD_mem_t type, haddr_t addr)
                 HDassert((addr + size) < file->iosize);
                 H5_CHECK_OVERFLOW(size, hsize_t, size_t);
                 HDmemset(&file->flavor[addr], H5FD_MEM_DEFAULT, (size_t)size);
-            } /* end if */
+            }
 
             /* Log the shrink like a free */
             if (file->fa.flags & H5FD_LOG_FREE)
                 HDfprintf(file->logfp,
                           "%10" PRIuHADDR "-%10" PRIuHADDR " (%10" PRIuHSIZE " bytes) (%s) Freed\n",
                           file->eoa, addr, size, flavors[type]);
-        } /* end if */
-    }     /* end if */
+        }
+    }
 
     file->eoa = addr;
 
@@ -1174,23 +1178,22 @@ static herr_t
 H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, size_t size,
                void *buf /*out*/)
 {
-    H5FD_log_t *  file       = (H5FD_log_t *)_file;
-    size_t        orig_size  = size; /* Save the original size for later */
-    haddr_t       orig_addr  = addr;
-    H5_timer_t    read_timer = {{0}, {0}, {0}, FALSE}; /* Timer for read operation */
-    H5_timevals_t read_times;                          /* Elapsed time for read operation */
-#ifndef H5_HAVE_PREADWRITE
-    H5_timer_t    seek_timer; /* Timer for seek operation */
-    H5_timevals_t seek_times; /* Elapsed time for seek operation */
-#endif                        /* H5_HAVE_PREADWRITE */
-    HDoff_t offset    = (HDoff_t)addr;
-    herr_t  ret_value = SUCCEED; /* Return value */
+    H5FD_log_t *  file      = (H5FD_log_t *)_file;
+    size_t        orig_size = size; /* Save the original size for later */
+    haddr_t       orig_addr = addr;
+    H5_timer_t    read_timer; /* Timer for read operation */
+    H5_timevals_t read_times; /* Elapsed time for read operation */
+    HDoff_t       offset    = (HDoff_t)addr;
+    herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_STATIC
 
     HDassert(file && file->pub.cls);
     HDassert(buf);
 
+    /* Initialize timer */
+    H5_timer_init(&read_timer);
+
     /* Check for overflow conditions */
     if (!H5F_addr_defined(addr))
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined, addr = %llu", (unsigned long long)addr)
@@ -1207,17 +1210,22 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
             HDassert((addr + size) < file->iosize);
             while (tmp_size-- > 0)
                 file->nread[tmp_addr++]++;
-        } /* end if */
-    }     /* end if */
+        }
+    }
 
 #ifndef H5_HAVE_PREADWRITE
     /* Seek to the correct location (if we don't have pread) */
     if (addr != file->pos || OP_READ != file->op) {
+
+        H5_timer_t    seek_timer; /* Timer for seek operation */
+        H5_timevals_t seek_times; /* Elapsed time for seek operation */
+
+        /* Initialize timer */
+        H5_timer_init(&seek_timer);
+
         /* Start timer for seek() call */
-        if (file->fa.flags & H5FD_LOG_TIME_SEEK) {
-            H5_timer_init(&seek_timer);
+        if (file->fa.flags & H5FD_LOG_TIME_SEEK)
             H5_timer_start(&seek_timer);
-        } /* end if */
 
         if (HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0)
             HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
@@ -1234,7 +1242,7 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
         if (file->fa.flags & H5FD_LOG_TIME_SEEK) {
             H5_timer_get_times(seek_timer, &seek_times);
             file->total_seek_time += seek_times.elapsed;
-        } /* end if */
+        }
 
         /* Emit log string if we're tracking individual seek events. */
         if (file->fa.flags & H5FD_LOG_LOC_SEEK) {
@@ -1248,15 +1256,13 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
                 HDfprintf(file->logfp, " (%fs @ %f)\n", seek_times.elapsed, seek_timer.initial.elapsed);
             else
                 HDfprintf(file->logfp, "\n");
-        } /* end if */
-    }     /* end if */
-#endif    /* H5_HAVE_PREADWRITE */
+        }
+    }
+#endif /* H5_HAVE_PREADWRITE */
 
     /* Start timer for read operation */
-    if (file->fa.flags & H5FD_LOG_TIME_READ) {
-        H5_timer_init(&read_timer);
+    if (file->fa.flags & H5FD_LOG_TIME_READ)
         H5_timer_start(&read_timer);
-    } /* end if */
 
     /*
      * Read data, being careful of interrupted system calls, partial results,
@@ -1301,13 +1307,13 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
                         HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf,
                         (unsigned long long)size, (unsigned long long)bytes_in,
                         (unsigned long long)bytes_read, (unsigned long long)offset);
-        } /* end if */
+        }
 
         if (0 == bytes_read) {
-            /* end of file but not end of format address space */
+            /* End of file but not end of format address space */
             HDmemset(buf, 0, size);
             break;
-        } /* end if */
+        }
 
         HDassert(bytes_read >= 0);
         HDassert((size_t)bytes_read <= size);
@@ -1315,8 +1321,7 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
         size -= (size_t)bytes_read;
         addr += (haddr_t)bytes_read;
         buf = (char *)buf + bytes_read;
-
-    } /* end while */
+    }
 
     /* Stop timer for read operation */
     if (file->fa.flags & H5FD_LOG_TIME_READ)
@@ -1330,7 +1335,7 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
     if (file->fa.flags & H5FD_LOG_TIME_READ) {
         H5_timer_get_times(read_timer, &read_times);
         file->total_read_time += read_times.elapsed;
-    } /* end if */
+    }
 
     /* Log information about the read */
     if (file->fa.flags & H5FD_LOG_LOC_READ) {
@@ -1344,7 +1349,7 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
             HDassert(type == H5FD_MEM_DEFAULT ||
                      type == (H5FD_mem_t)file->flavor[(orig_addr + orig_size) - 1] ||
                      (H5FD_mem_t)file->flavor[(orig_addr + orig_size) - 1] == H5FD_MEM_DEFAULT);
-        } /* end if */
+        }
 
         /* Add the read time, if we're tracking that.
          * Note that the read time is NOT emitted for when just H5FD_LOG_TIME_READ
@@ -1354,7 +1359,7 @@ H5FD__log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
             HDfprintf(file->logfp, " (%fs @ %f)\n", read_times.elapsed, read_timer.initial.elapsed);
         else
             HDfprintf(file->logfp, "\n");
-    } /* end if */
+    }
 
     /* Update current position */
     file->pos = addr;
@@ -1365,7 +1370,7 @@ done:
         /* Reset last file I/O information */
         file->pos = HADDR_UNDEF;
         file->op  = OP_UNKNOWN;
-    } /* end if */
+    }
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5FD__log_read() */
@@ -1388,17 +1393,13 @@ static herr_t
 H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, size_t size,
                 const void *buf)
 {
-    H5FD_log_t *  file        = (H5FD_log_t *)_file;
-    size_t        orig_size   = size; /* Save the original size for later */
-    haddr_t       orig_addr   = addr;
-    H5_timer_t    write_timer = {{0}, {0}, {0}, FALSE}; /* Timer for write operation */
-    H5_timevals_t write_times;                          /* Elapsed time for write operation */
-#ifndef H5_HAVE_PREADWRITE
-    H5_timer_t    seek_timer; /* Timer for seek operation */
-    H5_timevals_t seek_times; /* Elapsed time for seek operation */
-#endif                        /* H5_HAVE_PREADWRITE */
-    HDoff_t offset    = (HDoff_t)addr;
-    herr_t  ret_value = SUCCEED; /* Return value */
+    H5FD_log_t *  file      = (H5FD_log_t *)_file;
+    size_t        orig_size = size; /* Save the original size for later */
+    haddr_t       orig_addr = addr;
+    H5_timer_t    write_timer; /* Timer for write operation */
+    H5_timevals_t write_times; /* Elapsed time for write operation */
+    HDoff_t       offset    = (HDoff_t)addr;
+    herr_t        ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_STATIC
 
@@ -1406,13 +1407,16 @@ H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
     HDassert(size > 0);
     HDassert(buf);
 
+    /* Initialize timer */
+    H5_timer_init(&write_timer);
+
     /* Verify that we are writing out the type of data we allocated in this location */
     if (file->flavor) {
         HDassert(type == H5FD_MEM_DEFAULT || type == (H5FD_mem_t)file->flavor[addr] ||
                  (H5FD_mem_t)file->flavor[addr] == H5FD_MEM_DEFAULT);
         HDassert(type == H5FD_MEM_DEFAULT || type == (H5FD_mem_t)file->flavor[(addr + size) - 1] ||
                  (H5FD_mem_t)file->flavor[(addr + size) - 1] == H5FD_MEM_DEFAULT);
-    } /* end if */
+    }
 
     /* Check for overflow conditions */
     if (!H5F_addr_defined(addr))
@@ -1430,16 +1434,21 @@ H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
         HDassert((addr + size) < file->iosize);
         while (tmp_size-- > 0)
             file->nwrite[tmp_addr++]++;
-    } /* end if */
+    }
 
 #ifndef H5_HAVE_PREADWRITE
     /* Seek to the correct location (if we don't have pwrite) */
     if (addr != file->pos || OP_WRITE != file->op) {
+
+        H5_timer_t    seek_timer; /* Timer for seek operation */
+        H5_timevals_t seek_times; /* Elapsed time for seek operation */
+
+        /* Initialize timer */
+        H5_timer_init(&seek_timer);
+
         /* Start timer for seek() call */
-        if (file->fa.flags & H5FD_LOG_TIME_SEEK) {
-            H5_timer_init(&seek_timer);
+        if (file->fa.flags & H5FD_LOG_TIME_SEEK)
             H5_timer_start(&seek_timer);
-        } /* end if */
 
         if (HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0)
             HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
@@ -1456,7 +1465,7 @@ H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
         if (file->fa.flags & H5FD_LOG_TIME_SEEK) {
             H5_timer_get_times(seek_timer, &seek_times);
             file->total_seek_time += seek_times.elapsed;
-        } /* end if */
+        }
 
         /* Emit log string if we're tracking individual seek events. */
         if (file->fa.flags & H5FD_LOG_LOC_SEEK) {
@@ -1470,15 +1479,13 @@ H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
                 HDfprintf(file->logfp, " (%fs @ %f)\n", seek_times.elapsed, seek_timer.initial.elapsed);
             else
                 HDfprintf(file->logfp, "\n");
-        } /* end if */
-    }     /* end if */
-#endif    /* H5_HAVE_PREADWRITE */
+        }
+    }
+#endif /* H5_HAVE_PREADWRITE */
 
     /* Start timer for write operation */
-    if (file->fa.flags & H5FD_LOG_TIME_WRITE) {
-        H5_timer_init(&write_timer);
+    if (file->fa.flags & H5FD_LOG_TIME_WRITE)
         H5_timer_start(&write_timer);
-    } /* end if */
 
     /*
      * Write the data, being careful of interrupted system calls and partial
@@ -1545,7 +1552,7 @@ H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
     if (file->fa.flags & H5FD_LOG_TIME_WRITE) {
         H5_timer_get_times(write_timer, &write_times);
         file->total_write_time += write_times.elapsed;
-    } /* end if */
+    }
 
     /* Log information about the write */
     if (file->fa.flags & H5FD_LOG_LOC_WRITE) {
@@ -1558,8 +1565,8 @@ H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
             if ((H5FD_mem_t)file->flavor[orig_addr] == H5FD_MEM_DEFAULT) {
                 HDmemset(&file->flavor[orig_addr], (int)type, orig_size);
                 HDfprintf(file->logfp, " (fresh)");
-            } /* end if */
-        }     /* end if */
+            }
+        }
 
         /* Add the write time, if we're tracking that.
          * Note that the write time is NOT emitted for when just H5FD_LOG_TIME_WRITE
@@ -1569,7 +1576,7 @@ H5FD__log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, ha
             HDfprintf(file->logfp, " (%fs @ %f)\n", write_times.elapsed, write_timer.initial.elapsed);
         else
             HDfprintf(file->logfp, "\n");
-    } /* end if */
+    }
 
     /* Update current position and eof */
     file->pos = addr;
@@ -1582,7 +1589,7 @@ done:
         /* Reset last file I/O information */
         file->pos = HADDR_UNDEF;
         file->op  = OP_UNKNOWN;
-    } /* end if */
+    }
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5FD__log_write() */
@@ -1612,14 +1619,15 @@ H5FD__log_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_
 
     /* Extend the file to make sure it's large enough */
     if (!H5F_addr_eq(file->eoa, file->eof)) {
-        H5_timer_t    trunc_timer = {{0}, {0}, {0}, FALSE}; /* Timer for truncate operation */
-        H5_timevals_t trunc_times;                          /* Elapsed time for truncate operation */
+        H5_timer_t    trunc_timer; /* Timer for truncate operation */
+        H5_timevals_t trunc_times; /* Elapsed time for truncate operation */
+
+        /* Initialize timer */
+        H5_timer_init(&trunc_timer);
 
         /* Start timer for truncate operation */
-        if (file->fa.flags & H5FD_LOG_TIME_TRUNCATE) {
-            H5_timer_init(&trunc_timer);
+        if (file->fa.flags & H5FD_LOG_TIME_TRUNCATE)
             H5_timer_start(&trunc_timer);
-        } /* end if */
 
 #ifdef H5_HAVE_WIN32_API
         {
@@ -1643,7 +1651,7 @@ H5FD__log_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_
                 dwError = GetLastError();
                 if (dwError != NO_ERROR)
                     HGOTO_ERROR(H5E_FILE, H5E_FILEOPEN, FAIL, "unable to set file pointer")
-            } /* end if */
+            }
 
             if (0 == SetEndOfFile(file->hFile))
                 HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to extend file properly")
@@ -1666,7 +1674,7 @@ H5FD__log_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_
         if (file->fa.flags & H5FD_LOG_TIME_TRUNCATE) {
             H5_timer_get_times(trunc_timer, &trunc_times);
             file->total_truncate_time += trunc_times.elapsed;
-        } /* end if */
+        }
 
         /* Emit log string if we're tracking individual truncate events. */
         if (file->fa.flags & H5FD_LOG_TRUNCATE) {
@@ -1680,7 +1688,7 @@ H5FD__log_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_
                 HDfprintf(file->logfp, " (%fs @ %f)\n", trunc_times.elapsed, trunc_timer.initial.elapsed);
             else
                 HDfprintf(file->logfp, "\n");
-        } /* end if */
+        }
 
         /* Update the eof value */
         file->eof = file->eoa;