Align with "parallel fence" changes (#479)

* Small code updates and simplifications

* Committing clang-format changes

* Fix 'make installcheck' for parallel builds

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

9 files changed, 86 insertions, 163 deletions

diff --git a/src/H5AC.c b/src/H5AC.c
index ffdca78..2eadd21 100644
--- a/src/H5AC.c
+++ b/src/H5AC.c
@@ -350,19 +350,14 @@ H5AC_create(const H5F_t *f, H5AC_cache_config_t *config_ptr, H5AC_cache_image_co
         if (NULL == (aux_ptr->candidate_slist_ptr = H5SL_create(H5SL_TYPE_HADDR, NULL)))
             HGOTO_ERROR(H5E_CACHE, H5E_CANTCREATE, FAIL, "can't create candidate entry list")
 
-        if (aux_ptr != NULL)
-            if (aux_ptr->mpi_rank == 0)
-                f->shared->cache = H5C_create(H5AC__DEFAULT_MAX_CACHE_SIZE, H5AC__DEFAULT_MIN_CLEAN_SIZE,
-                                              (H5AC_NTYPES - 1), H5AC_class_s, H5AC__check_if_write_permitted,
-                                              TRUE, H5AC__log_flushed_entry, (void *)aux_ptr);
-            else
-                f->shared->cache =
-                    H5C_create(H5AC__DEFAULT_MAX_CACHE_SIZE, H5AC__DEFAULT_MIN_CLEAN_SIZE, (H5AC_NTYPES - 1),
-                               H5AC_class_s, H5AC__check_if_write_permitted, TRUE, NULL, (void *)aux_ptr);
+        if (aux_ptr->mpi_rank == 0)
+            f->shared->cache = H5C_create(H5AC__DEFAULT_MAX_CACHE_SIZE, H5AC__DEFAULT_MIN_CLEAN_SIZE,
+                                          (H5AC_NTYPES - 1), H5AC_class_s, H5AC__check_if_write_permitted,
+                                          TRUE, H5AC__log_flushed_entry, (void *)aux_ptr);
         else
             f->shared->cache =
                 H5C_create(H5AC__DEFAULT_MAX_CACHE_SIZE, H5AC__DEFAULT_MIN_CLEAN_SIZE, (H5AC_NTYPES - 1),
-                           H5AC_class_s, H5AC__check_if_write_permitted, TRUE, NULL, NULL);
+                           H5AC_class_s, H5AC__check_if_write_permitted, TRUE, NULL, (void *)aux_ptr);
     } /* end if */
     else {
 #endif /* H5_HAVE_PARALLEL */
diff --git a/src/H5ACmpio.c b/src/H5ACmpio.c
index 140fd96..7d2ba25 100644
--- a/src/H5ACmpio.c
+++ b/src/H5ACmpio.c
@@ -1271,7 +1271,7 @@ H5AC__propagate_and_apply_candidate_list(H5F_t *f)
         if (aux_ptr->write_done)
             (aux_ptr->write_done)();
 
-        /* to prevent "messages from the past" we must synchronize all
+        /* To prevent "messages from the past" we must synchronize all
          * processes again before we go on.
          */
         if (MPI_SUCCESS != (mpi_result = MPI_Barrier(aux_ptr->mpi_comm)))
@@ -1514,7 +1514,7 @@ H5AC__receive_and_apply_clean_list(H5F_t *f)
         HGOTO_ERROR(H5E_CACHE, H5E_CANTGET, FAIL, "can't receive clean list")
 
     if (num_entries > 0)
-        /* mark the indicated entries as clean */
+        /* Mark the indicated entries as clean */
         if (H5C_mark_entries_as_clean(f, num_entries, haddr_buf_ptr) < 0)
             HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't mark entries clean.")
 
@@ -1900,28 +1900,22 @@ H5AC__rsp__p0_only__flush(H5F_t *f)
 
         /* Check for error on the write operation */
         if (result < 0)
-
             HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't flush.")
 
         /* this code exists primarily for the test bed -- it allows us to
          * enforce POSIX semantics on the server that pretends to be a
          * file system in our parallel tests.
          */
-        if (aux_ptr->write_done) {
-
+        if (aux_ptr->write_done)
             (aux_ptr->write_done)();
-        }
     } /* end if */
 
     /* Propagate cleaned entries to other ranks. */
     if (H5AC__propagate_flushed_and_still_clean_entries_list(f) < 0)
-
         HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't propagate clean entries list.")
 
 done:
-
     FUNC_LEAVE_NOAPI(ret_value)
-
 } /* H5AC__rsp__p0_only__flush() */
 
 /*-------------------------------------------------------------------------
diff --git a/src/H5C.c b/src/H5C.c
index 551a2b2..1b885e3 100644
--- a/src/H5C.c
+++ b/src/H5C.c
@@ -21,14 +21,8 @@
  *              things which exist on disk, and which may be
  *              unambiguously referenced by their disk addresses.
  *
- *              The code in this module was initially written in
- *        support of a complete re-write of the metadata cache
- *        in H5AC.c  However, other uses for the cache code
- *        suggested themselves, and thus this file was created
- *        in an attempt to support re-use.
- *
- *        For a detailed overview of the cache, please see the
- *        header comment for H5C_t in H5Cpkg.h.
+ *		For a detailed overview of the cache, please see the
+ *		header comment for H5C_t in H5Cpkg.h.
  *
  *-------------------------------------------------------------------------
  */
@@ -39,9 +33,7 @@
  *
  *    Code Changes:
  *
- *     - Remove extra functionality in H5C__flush_single_entry()?
- *
- *     - Change protect/unprotect to lock/unlock.
+ *	 - Change protect/unprotect to lock/unlock.
  *
  *     - Flush entries in increasing address order in
  *       H5C__make_space_in_cache().
@@ -53,18 +45,9 @@
  *       I/O overhead.  Can't do this just yet as some entries are not
  *       contiguous.  Do this in parallel only or in serial as well?
  *
- *     - Create MPI type for dirty objects when flushing in parallel.
- *
- *     - Now that TBBT routines aren't used, fix nodes in memory to
- *         point directly to the skip list node from the LRU list, eliminating
- *         skip list lookups when evicting objects from the cache.
- *
- *    Tests:
- *
- *     - Trim execution time.  (This is no longer a major issue with the
- *       shift from the TBBT to a hash table for indexing.)
- *
- *     - Add random tests.
+ *	 - Fix nodes in memory to point directly to the skip list node from
+ *         the LRU list, eliminating skip list lookups when evicting objects
+ *         from the cache.
  *
  **************************************************************************/
 
@@ -6650,9 +6633,7 @@ H5C__flush_single_entry(H5F_t *f, H5C_cache_entry_t *entry_ptr, unsigned flags)
                 }
 
                 if (H5F_block_write(f, mem_type, entry_ptr->addr, entry_ptr->size, entry_ptr->image_ptr) < 0)
-
                     HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "Can't write image to file")
-
 #ifdef H5_HAVE_PARALLEL
             }
 #endif /* H5_HAVE_PARALLEL */
diff --git a/src/H5Cmpio.c b/src/H5Cmpio.c
index 7a5c630..66c6601 100644
--- a/src/H5Cmpio.c
+++ b/src/H5Cmpio.c
@@ -154,19 +154,12 @@ static herr_t H5C__flush_candidates_in_ring(H5F_t *f, H5C_ring_t ring, unsigned
  * Programmer:  John Mainzer
  *              3/17/10
  *
- * Changes:     Updated sanity checks to allow for the possibility that
- *              the slist is disabled.
- *                                               JRM -- 8/3/20
- *
  *-------------------------------------------------------------------------
  */
 herr_t
 H5C_apply_candidate_list(H5F_t *f, H5C_t *cache_ptr, unsigned num_candidates, haddr_t *candidates_list_ptr,
                          int mpi_rank, int mpi_size)
 {
-    int                i;
-    int                m;
-    unsigned           n;
     unsigned           first_entry_to_flush;
     unsigned           last_entry_to_flush;
     unsigned           total_entries_to_clear     = 0;
@@ -176,15 +169,13 @@ H5C_apply_candidate_list(H5F_t *f, H5C_t *cache_ptr, unsigned num_candidates, ha
     unsigned           entries_to_clear[H5C_RING_NTYPES];
     haddr_t            addr;
     H5C_cache_entry_t *entry_ptr = NULL;
-
 #if H5C_DO_SANITY_CHECKS
     haddr_t last_addr;
 #endif /* H5C_DO_SANITY_CHECKS */
-
 #if H5C_APPLY_CANDIDATE_LIST__DEBUG
     char tbl_buf[1024];
 #endif /* H5C_APPLY_CANDIDATE_LIST__DEBUG */
-
+    unsigned m, n;
     unsigned u;                   /* Local index variable */
     herr_t   ret_value = SUCCEED; /* Return value */
 
@@ -226,9 +217,7 @@ H5C_apply_candidate_list(H5F_t *f, H5C_t *cache_ptr, unsigned num_candidates, ha
     } /* end if */
 
     n = num_candidates / (unsigned)mpi_size;
-    if (num_candidates % (unsigned)mpi_size > INT_MAX)
-        HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "m overflow")
-    m = (int)(num_candidates % (unsigned)mpi_size);
+    m = num_candidates % (unsigned)mpi_size;
 
     if (NULL ==
         (candidate_assignment_table = (unsigned *)H5MM_malloc(sizeof(unsigned) * (size_t)(mpi_size + 1))))
@@ -239,31 +228,31 @@ H5C_apply_candidate_list(H5F_t *f, H5C_t *cache_ptr, unsigned num_candidates, ha
     candidate_assignment_table[mpi_size] = num_candidates;
 
     if (m == 0) { /* mpi_size is an even divisor of num_candidates */
-        for (i = 1; i < mpi_size; i++)
-            candidate_assignment_table[i] = candidate_assignment_table[i - 1] + n;
+        for (u = 1; u < (unsigned)mpi_size; u++)
+            candidate_assignment_table[u] = candidate_assignment_table[u - 1] + n;
     } /* end if */
     else {
-        for (i = 1; i <= m; i++)
-            candidate_assignment_table[i] = candidate_assignment_table[i - 1] + n + 1;
+        for (u = 1; u <= m; u++)
+            candidate_assignment_table[u] = candidate_assignment_table[u - 1] + n + 1;
 
         if (num_candidates < (unsigned)mpi_size) {
-            for (i = m + 1; i < mpi_size; i++)
-                candidate_assignment_table[i] = num_candidates;
+            for (u = m + 1; u < (unsigned)mpi_size; u++)
+                candidate_assignment_table[u] = num_candidates;
         } /* end if */
         else {
-            for (i = m + 1; i < mpi_size; i++)
-                candidate_assignment_table[i] = candidate_assignment_table[i - 1] + n;
+            for (u = m + 1; u < (unsigned)mpi_size; u++)
+                candidate_assignment_table[u] = candidate_assignment_table[u - 1] + n;
         } /* end else */
     }     /* end else */
     HDassert((candidate_assignment_table[mpi_size - 1] + n) == num_candidates);
 
 #if H5C_DO_SANITY_CHECKS
     /* Verify that the candidate assignment table has the expected form */
-    for (i = 1; i < mpi_size - 1; i++) {
+    for (u = 1; u < (unsigned)(mpi_size - 1); u++) {
         unsigned a, b;
 
-        a = candidate_assignment_table[i] - candidate_assignment_table[i - 1];
-        b = candidate_assignment_table[i + 1] - candidate_assignment_table[i];
+        a = candidate_assignment_table[u] - candidate_assignment_table[u - 1];
+        b = candidate_assignment_table[u + 1] - candidate_assignment_table[u];
 
         HDassert(n + 1 >= a);
         HDassert(a >= b);
@@ -275,11 +264,11 @@ H5C_apply_candidate_list(H5F_t *f, H5C_t *cache_ptr, unsigned num_candidates, ha
     last_entry_to_flush  = candidate_assignment_table[mpi_rank + 1] - 1;
 
 #if H5C_APPLY_CANDIDATE_LIST__DEBUG
-    for (i = 0; i < 1024; i++)
-        tbl_buf[i] = '\0';
+    for (u = 0; u < 1024; u++)
+        tbl_buf[u] = '\0';
     HDsprintf(&(tbl_buf[0]), "candidate assignment table = ");
-    for (i = 0; i <= mpi_size; i++)
-        HDsprintf(&(tbl_buf[HDstrlen(tbl_buf)]), " %u", candidate_assignment_table[i]);
+    for (u = 0; u <= (unsigned)mpi_size; u++)
+        HDsprintf(&(tbl_buf[HDstrlen(tbl_buf)]), " %u", candidate_assignment_table[u]);
     HDsprintf(&(tbl_buf[HDstrlen(tbl_buf)]), "\n");
     HDfprintf(stdout, "%s", tbl_buf);
 
@@ -354,9 +343,9 @@ H5C_apply_candidate_list(H5F_t *f, H5C_t *cache_ptr, unsigned num_candidates, ha
 #if H5C_DO_SANITY_CHECKS
     m = 0;
     n = 0;
-    for (i = 0; i < H5C_RING_NTYPES; i++) {
-        m += (int)entries_to_flush[i];
-        n += entries_to_clear[i];
+    for (u = 0; u < H5C_RING_NTYPES; u++) {
+        m += entries_to_flush[u];
+        n += entries_to_clear[u];
     } /* end if */
 
     HDassert((unsigned)m == total_entries_to_flush);
@@ -957,10 +946,8 @@ H5C__collective_write(H5F_t *f)
     int *            length_array = NULL;
     MPI_Aint *       buf_array    = NULL;
     MPI_Aint *       offset_array = NULL;
-    MPI_Datatype     btype;
-    hbool_t          btype_created = FALSE;
-    MPI_Datatype     ftype;
-    hbool_t          ftype_created = FALSE;
+    MPI_Datatype     btype        = MPI_BYTE;
+    MPI_Datatype     ftype        = MPI_BYTE;
     int              mpi_code;
     char             unused = 0; /* Unused, except for non-NULL pointer value */
     size_t           buf_count;
@@ -1032,7 +1019,6 @@ H5C__collective_write(H5F_t *f)
         if (MPI_SUCCESS !=
             (mpi_code = MPI_Type_create_hindexed(count, length_array, buf_array, MPI_BYTE, &btype)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
-        btype_created = TRUE;
         if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&btype)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
 
@@ -1040,7 +1026,6 @@ H5C__collective_write(H5F_t *f)
         if (MPI_SUCCESS !=
             (mpi_code = MPI_Type_create_hindexed(count, length_array, offset_array, MPI_BYTE, &ftype)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
-        ftype_created = TRUE;
         if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&ftype)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
 
@@ -1048,10 +1033,6 @@ H5C__collective_write(H5F_t *f)
         buf_count = 1;
     } /* end if */
     else {
-        /* Pass trivial buf type, file type to the file driver */
-        btype = MPI_BYTE;
-        ftype = MPI_BYTE;
-
         /* Set non-NULL pointer for I/O operation */
         base_buf = &unused;
 
@@ -1074,9 +1055,9 @@ done:
     offset_array = (MPI_Aint *)H5MM_xfree(offset_array);
 
     /* Free MPI Types */
-    if (btype_created && MPI_SUCCESS != (mpi_code = MPI_Type_free(&btype)))
+    if (MPI_BYTE != btype && MPI_SUCCESS != (mpi_code = MPI_Type_free(&btype)))
         HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
-    if (ftype_created && MPI_SUCCESS != (mpi_code = MPI_Type_free(&ftype)))
+    if (MPI_BYTE != ftype && MPI_SUCCESS != (mpi_code = MPI_Type_free(&ftype)))
         HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
 
     /* Reset transfer mode in API context, if changed */
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index f0a6842..f79b9cd 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -750,18 +750,18 @@ done:
 static H5FD_t *
 H5FD__mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR_UNUSED maxaddr)
 {
-    H5FD_mpio_t *   file = NULL;
-    MPI_File        fh;
-    hbool_t         file_opened = FALSE; /* Flag to indicate that the file was successfully opened */
-    int             mpi_amode;
-    int             mpi_rank; /* MPI rank of this process */
-    int             mpi_size; /* Total number of MPI processes */
-    int             mpi_code; /* MPI return code */
-    MPI_Offset      size;
-    H5P_genplist_t *plist; /* Property list pointer */
-    MPI_Comm        comm      = MPI_COMM_NULL;
-    MPI_Info        info      = MPI_INFO_NULL;
-    H5FD_t *        ret_value = NULL; /* Return value */
+    H5FD_mpio_t *   file = NULL;          /* VFD File struct for new file */
+    H5P_genplist_t *plist;                /* Property list pointer */
+    MPI_Comm        comm = MPI_COMM_NULL; /* MPI Communicator, from plist */
+    MPI_Info        info = MPI_INFO_NULL; /* MPI Info, from plist */
+    MPI_File        fh;                   /* MPI file handle */
+    hbool_t         file_opened = FALSE;  /* Flag to indicate that the file was successfully opened */
+    int             mpi_amode;            /* MPI file access flags */
+    int             mpi_rank = INT_MAX;   /* MPI rank of this process */
+    int             mpi_size;             /* Total number of MPI processes */
+    int             mpi_code;             /* MPI return code */
+    MPI_Offset      file_size;            /* File size (of existing files) */
+    H5FD_t *        ret_value = NULL;     /* Return value */
 
     FUNC_ENTER_STATIC
 
@@ -781,6 +781,12 @@ H5FD__mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR
     if (H5P_get(plist, H5F_ACS_MPI_PARAMS_INFO_NAME, &info) < 0)
         HGOTO_ERROR(H5E_VFL, H5E_CANTGET, NULL, "can't get MPI info object")
 
+    /* Get the MPI rank of this process and the total number of processes */
+    if (MPI_SUCCESS != (mpi_code = MPI_Comm_rank(comm, &mpi_rank)))
+        HMPI_GOTO_ERROR(NULL, "MPI_Comm_rank failed", mpi_code)
+    if (MPI_SUCCESS != (mpi_code = MPI_Comm_size(comm, &mpi_size)))
+        HMPI_GOTO_ERROR(NULL, "MPI_Comm_size failed", mpi_code)
+
     /* Convert HDF5 flags to MPI-IO flags */
     /* Some combinations are illegal; let MPI-IO figure it out */
     mpi_amode = (flags & H5F_ACC_RDWR) ? MPI_MODE_RDWR : MPI_MODE_RDONLY;
@@ -810,12 +816,6 @@ H5FD__mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR
         HMPI_GOTO_ERROR(NULL, "MPI_File_open failed", mpi_code)
     file_opened = TRUE;
 
-    /* Get the MPI rank of this process and the total number of processes */
-    if (MPI_SUCCESS != (mpi_code = MPI_Comm_rank(comm, &mpi_rank)))
-        HMPI_GOTO_ERROR(NULL, "MPI_Comm_rank failed", mpi_code)
-    if (MPI_SUCCESS != (mpi_code = MPI_Comm_size(comm, &mpi_size)))
-        HMPI_GOTO_ERROR(NULL, "MPI_Comm_size failed", mpi_code)
-
     /* Build the return value and initialize it */
     if (NULL == (file = (H5FD_mpio_t *)H5MM_calloc(sizeof(H5FD_mpio_t))))
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
@@ -826,17 +826,16 @@ H5FD__mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR
     file->mpi_size = mpi_size;
 
     /* Only processor p0 will get the filesize and broadcast it. */
-    if (mpi_rank == 0) {
-        if (MPI_SUCCESS != (mpi_code = MPI_File_get_size(fh, &size)))
+    if (mpi_rank == 0)
+        if (MPI_SUCCESS != (mpi_code = MPI_File_get_size(fh, &file_size)))
             HMPI_GOTO_ERROR(NULL, "MPI_File_get_size failed", mpi_code)
-    } /* end if */
 
     /* Broadcast file size */
-    if (MPI_SUCCESS != (mpi_code = MPI_Bcast(&size, (int)sizeof(MPI_Offset), MPI_BYTE, 0, comm)))
+    if (MPI_SUCCESS != (mpi_code = MPI_Bcast(&file_size, (int)sizeof(MPI_Offset), MPI_BYTE, 0, comm)))
         HMPI_GOTO_ERROR(NULL, "MPI_Bcast failed", mpi_code)
 
     /* Determine if the file should be truncated */
-    if (size && (flags & H5F_ACC_TRUNC)) {
+    if (file_size && (flags & H5F_ACC_TRUNC)) {
         if (MPI_SUCCESS != (mpi_code = MPI_File_set_size(fh, (MPI_Offset)0)))
             HMPI_GOTO_ERROR(NULL, "MPI_File_set_size failed", mpi_code)
 
@@ -845,11 +844,11 @@ H5FD__mpio_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t H5_ATTR
             HMPI_GOTO_ERROR(NULL, "MPI_Barrier failed", mpi_code)
 
         /* File is zero size now */
-        size = 0;
+        file_size = 0;
     } /* end if */
 
     /* Set the size of the file (from library's perspective) */
-    file->eof       = H5FD_mpi_MPIOff_to_haddr(size);
+    file->eof       = H5FD_mpi_MPIOff_to_haddr(file_size);
     file->local_eof = file->eof;
 
     /* Set return value */
@@ -906,7 +905,7 @@ H5FD__mpio_close(H5FD_t *_file)
     HDassert(H5FD_MPIO == file->pub.driver_id);
 
     /* MPI_File_close sets argument to MPI_FILE_NULL */
-    if (MPI_SUCCESS != (mpi_code = MPI_File_close(&(file->f) /*in,out*/)))
+    if (MPI_SUCCESS != (mpi_code = MPI_File_close(&(file->f))))
         HMPI_GOTO_ERROR(FAIL, "MPI_File_close failed", mpi_code)
 
     /* Clean up other stuff */
@@ -1228,8 +1227,10 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
                 if (MPI_SUCCESS != (mpi_code = MPI_Bcast(buf, size_i, buf_type, 0, file->comm)))
                     HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code)
             } /* end if */
-            else if (MPI_SUCCESS !=
-                     (mpi_code = MPI_File_read_at_all(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat)))
+            else
+                /* Perform collective read operation */
+                if (MPI_SUCCESS !=
+                    (mpi_code = MPI_File_read_at_all(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat)))
                 HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at_all failed", mpi_code)
         } /* end if */
         else {
@@ -1238,6 +1239,7 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
                 HDfprintf(stdout, "%s: doing MPI independent IO\n", FUNC);
 #endif
 
+            /* Perform independent read operation */
             if (MPI_SUCCESS !=
                 (mpi_code = MPI_File_read_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat)))
                 HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at failed", mpi_code)
@@ -1250,7 +1252,9 @@ H5FD__mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
                                                          H5FD_mpi_native_g, file->info)))
             HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
     } /* end if */
-    else if (MPI_SUCCESS != (mpi_code = MPI_File_read_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat)))
+    else
+        /* Perform independent read operation */
+        if (MPI_SUCCESS != (mpi_code = MPI_File_read_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat)))
         HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at failed", mpi_code)
 
     /* Only retrieve bytes read if this rank _actually_ participated in I/O */
@@ -1446,6 +1450,7 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h
             if (H5FD_mpio_Debug[(int)'w'])
                 HDfprintf(stdout, "%s: doing MPI collective IO\n", FUNC);
 #endif
+            /* Perform collective write operation */
             if (MPI_SUCCESS !=
                 (mpi_code = MPI_File_write_at_all(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat)))
                 HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at_all failed", mpi_code)
@@ -1458,6 +1463,7 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h
             if (H5FD_mpio_Debug[(int)'w'])
                 HDfprintf(stdout, "%s: doing MPI independent IO\n", FUNC);
 #endif
+            /* Perform independent write operation */
             if (MPI_SUCCESS !=
                 (mpi_code = MPI_File_write_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat)))
                 HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at failed", mpi_code)
@@ -1468,8 +1474,9 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h
                                                          H5FD_mpi_native_g, file->info)))
             HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
     } /* end if */
-    else if (MPI_SUCCESS !=
-             (mpi_code = MPI_File_write_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat)))
+    else
+        /* Perform independent write operation */
+        if (MPI_SUCCESS != (mpi_code = MPI_File_write_at(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat)))
         HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at failed", mpi_code)
 
         /* How many bytes were actually written? */
@@ -1507,9 +1514,9 @@ H5FD__mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, h
         file->local_eof = addr + (haddr_t)bytes_written;
 
 done:
-    if (derived_type) {
+    if (derived_type)
         MPI_Type_free(&buf_type);
-    }
+
 #ifdef H5FDmpio_DEBUG
     if (H5FD_mpio_Debug[(int)'t'])
         HDfprintf(stdout, "%s: Leaving, proc %d: ret_value = %d\n", FUNC, file->mpi_rank, ret_value);
@@ -1569,13 +1576,14 @@ done:
  *
  *              This is a little sticky in the mpio case, as it is not
  *              easy for us to track the current EOF by extracting it from
- *              write calls.
+ *              write calls, since other ranks could have written to the
+ *              file beyond the local EOF.
  *
- *              Instead, we first check to see if the eoa has changed since
+ *              Instead, we first check to see if the EOA has changed since
  *              the last call to this function.  If it has, we call
  *              MPI_File_get_size() to determine the current EOF, and
  *              only call MPI_File_set_size() if this value disagrees
- *              with the current eoa.
+ *              with the current EOA.
  *
  * Return:      SUCCEED/FAIL
  *
@@ -1637,7 +1645,7 @@ H5FD__mpio_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR
         if (H5FD_mpi_haddr_to_MPIOff(file->eoa, &needed_eof) < 0)
             HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "cannot convert from haddr_t to MPI_Offset")
 
-        /* eoa != eof.  Set eof to eoa */
+        /* EOA != EOF.  Set EOF to EOA */
         if (size != needed_eof) {
             /* Extend the file's size */
             if (MPI_SUCCESS != (mpi_code = MPI_File_set_size(file->f, needed_eof)))
@@ -1749,5 +1757,4 @@ H5FD__mpio_communicator(const H5FD_t *_file)
 
     FUNC_LEAVE_NOAPI(file->comm)
 } /* end H5FD__mpio_communicator() */
-
 #endif /* H5_HAVE_PARALLEL */
diff --git a/src/H5Fint.c b/src/H5Fint.c
index 6da9473..ed6b9c1 100644
--- a/src/H5Fint.c
+++ b/src/H5Fint.c
@@ -81,6 +81,7 @@ static herr_t H5F__build_name(const char *prefix, const char *file_name, char **
 static char * H5F__getenv_prefix_name(char **env_prefix /*in,out*/);
 static H5F_t *H5F__new(H5F_shared_t *shared, unsigned flags, hid_t fcpl_id, hid_t fapl_id, H5FD_t *lf);
 static herr_t H5F__check_if_using_file_locks(H5P_genplist_t *fapl, hbool_t *use_file_locking);
+static herr_t H5F__dest(H5F_t *f, hbool_t flush);
 static herr_t H5F__build_actual_name(const H5F_t *f, const H5P_genplist_t *fapl, const char *name,
                                      char ** /*out*/ actual_name);
 static herr_t H5F__flush_phase1(H5F_t *f);
@@ -1379,12 +1380,12 @@ done:
  * Return:      SUCCEED/FAIL
  *-------------------------------------------------------------------------
  */
-herr_t
+static herr_t
 H5F__dest(H5F_t *f, hbool_t flush)
 {
     herr_t ret_value = SUCCEED; /* Return value */
 
-    FUNC_ENTER_PACKAGE
+    FUNC_ENTER_STATIC
 
     /* Sanity check */
     HDassert(f);
@@ -2512,11 +2513,6 @@ H5F_try_close(H5F_t *f, hbool_t *was_closed /*out*/)
         if (H5F__efc_try_close(f) < 0)
             HGOTO_ERROR(H5E_FILE, H5E_CANTRELEASE, FAIL, "can't attempt to close EFC")
 
-    /* Delay flush until the shared file struct is closed, in H5F__dest.  If the
-     * application called H5Fclose, it would have been flushed in that function
-     * (unless it will have been flushed in H5F__dest anyways).
-     */
-
     /* Destroy the H5F_t struct and decrement the reference count for the
      * shared H5F_shared_t struct. If the reference count for the H5F_shared_t
      * struct reaches zero then destroy it also.
diff --git a/src/H5Fmpi.c b/src/H5Fmpi.c
index 3336d4f..4b5283e 100644
--- a/src/H5Fmpi.c
+++ b/src/H5Fmpi.c
@@ -68,35 +68,6 @@
 /*******************/
 
 #ifdef H5_HAVE_PARALLEL
-
-/*-------------------------------------------------------------------------
- * Function:    H5F_get_mpi_handle
- *
- * Purpose:     Retrieves MPI File handle.
- *
- * Return:      Success:        The size (positive)
- *              Failure:        Negative
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5F_get_mpi_handle(const H5F_t *f, MPI_File **f_handle)
-{
-    herr_t ret_value = SUCCEED;
-    hid_t  fapl_id   = H5I_INVALID_HID;
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    HDassert(f && f->shared);
-
-    /* Dispatch to driver */
-    if ((ret_value = H5FD_get_vfd_handle(f->shared->lf, fapl_id, (void **)f_handle)) < 0)
-        HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get mpi file handle")
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5F_get_mpi_handle() */
-
 /*-------------------------------------------------------------------------
  * Function:    H5F_mpi_get_rank
  *
diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h
index 371260d..087c9c9 100644
--- a/src/H5Fpkg.h
+++ b/src/H5Fpkg.h
@@ -405,7 +405,6 @@ H5_DLLVAR htri_t use_locks_env_g;
 /* General routines */
 H5_DLL herr_t H5F__post_open(H5F_t *f);
 H5_DLL H5F_t * H5F__reopen(H5F_t *f);
-H5_DLL herr_t  H5F__dest(H5F_t *f, hbool_t flush);
 H5_DLL herr_t  H5F__flush(H5F_t *f);
 H5_DLL htri_t  H5F__is_hdf5(const char *name, hid_t fapl_id);
 H5_DLL ssize_t H5F__get_file_image(H5F_t *f, void *buf_ptr, size_t buf_len);
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 0c75cf0..5c5937b 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -955,7 +955,6 @@ H5_DLL herr_t H5F_eoa_dirty(H5F_t *f);
 
 /* Parallel I/O (i.e. MPI) related routines */
 #ifdef H5_HAVE_PARALLEL
-H5_DLL herr_t   H5F_get_mpi_handle(const H5F_t *f, MPI_File **f_handle);
 H5_DLL int      H5F_mpi_get_rank(const H5F_t *f);
 H5_DLL MPI_Comm H5F_mpi_get_comm(const H5F_t *f);
 H5_DLL int      H5F_shared_mpi_get_size(const H5F_shared_t *f_sh);