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

hl/src/H5PT.c

@@ -29,7 +29,7 @@ static H5I_type_t H5PT_ptable_id_type = H5I_UNINIT;
 #define H5PT_HASH_TABLE_SIZE 64
 
 /* Packet Table private functions */
-static herr_t H5PT_free_id(void *id, void **_ctx);
+static herr_t H5PT_free_id(void *id);
 static herr_t H5PT_close(htbl_t *table);
 static herr_t H5PT_create_index(htbl_t *table_id);
 static herr_t H5PT_set_index(htbl_t *table_id, hsize_t pt_index);
@@ -87,8 +87,7 @@ H5PTcreate(hid_t loc_id, const char *dset_name, hid_t dtype_id, hsize_t chunk_si
 
     /* Register the packet table ID type if this is the first table created */
     if (H5PT_ptable_id_type < 0)
-        if ((H5PT_ptable_id_type =
-                 H5Iregister_type((size_t)H5PT_HASH_TABLE_SIZE, 0, (H5I_free_t)H5PT_free_id)) < 0)
+        if ((H5PT_ptable_id_type = H5Iregister_type((size_t)H5PT_HASH_TABLE_SIZE, 0, H5PT_free_id)) < 0)
             goto error;
 
     /* Get memory for the table identifier */
@@ -208,8 +207,7 @@ H5PTcreate_fl(hid_t loc_id, const char *dset_name, hid_t dtype_id, hsize_t chunk
 
     /* Register the packet table ID type if this is the first table created */
     if (H5PT_ptable_id_type < 0)
-        if ((H5PT_ptable_id_type =
-                 H5Iregister_type((size_t)H5PT_HASH_TABLE_SIZE, 0, (H5I_free_t)H5PT_free_id)) < 0)
+        if ((H5PT_ptable_id_type = H5Iregister_type((size_t)H5PT_HASH_TABLE_SIZE, 0, H5PT_free_id)) < 0)
             goto error;
 
     /* Get memory for the table identifier */
@@ -323,8 +321,7 @@ H5PTopen(hid_t loc_id, const char *dset_name)
 
     /* Register the packet table ID type if this is the first table created */
     if (H5PT_ptable_id_type < 0)
-        if ((H5PT_ptable_id_type =
-                 H5Iregister_type((size_t)H5PT_HASH_TABLE_SIZE, 0, (H5I_free_t)H5PT_free_id)) < 0)
+        if ((H5PT_ptable_id_type = H5Iregister_type((size_t)H5PT_HASH_TABLE_SIZE, 0, H5PT_free_id)) < 0)
             goto error;
 
     table = (htbl_t *)HDmalloc(sizeof(htbl_t));
@@ -402,7 +399,7 @@ H5PTopen(hid_t loc_id, const char *dset_name)
  *-------------------------------------------------------------------------
  */
 static herr_t
-H5PT_free_id(void *id, void H5_ATTR_UNUSED **_ctx)
+H5PT_free_id(void *id)
 {
     HDfree(id);
     return SUCCEED;

src/H5B2int.c

@@ -52,9 +52,9 @@
 /********************/
 /* Local Prototypes */
 /********************/
-static herr_t H5B2__update_child_flush_depends(H5B2_hdr_t *hdr, unsigned depth,
-                                               const H5B2_node_ptr_t *node_ptrs, unsigned start_idx,
-                                               unsigned end_idx, void *old_parent, void *new_parent);
+static herr_t H5B2__update_child_flush_depends(H5B2_hdr_t *hdr, unsigned depth, H5B2_node_ptr_t *node_ptrs,
+                                               unsigned start_idx, unsigned end_idx, void *old_parent,
+                                               void *new_parent);
 
 /*********************/
 /* Package Variables */
@@ -1617,7 +1617,7 @@ H5B2__insert(H5B2_hdr_t *hdr, void *udata)
  *-------------------------------------------------------------------------
  */
 herr_t
-H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_node, void *parent,
+H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node, void *parent,
                    H5B2_operator_t op, void *op_data)
 {
     const H5AC_class_t *curr_node_class = NULL;   /* Pointer to current node's class info */
@@ -1642,8 +1642,7 @@ H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_
 
         /* Lock the current B-tree node */
         if (NULL ==
-            (internal = H5B2__protect_internal(hdr, parent, (H5B2_node_ptr_t *)curr_node, depth, FALSE,
-                                               H5AC__READ_ONLY_FLAG))) /* Casting away const OK -QAK */
+            (internal = H5B2__protect_internal(hdr, parent, curr_node, depth, FALSE, H5AC__READ_ONLY_FLAG)))
             HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect B-tree internal node")
 
         /* Set up information about current node */
@@ -1739,8 +1738,8 @@ H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_
  *-------------------------------------------------------------------------
  */
 herr_t
-H5B2__delete_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_node, void *parent,
-                  H5B2_remove_t op, void *op_data)
+H5B2__delete_node(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node, void *parent, H5B2_remove_t op,
+                  void *op_data)
 {
     const H5AC_class_t *curr_node_class = NULL; /* Pointer to current node's class info */
     void *              node            = NULL; /* Pointers to current node */
@@ -1759,8 +1758,7 @@ H5B2__delete_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_n
 
         /* Lock the current B-tree node */
         if (NULL ==
-            (internal = H5B2__protect_internal(hdr, parent, (H5B2_node_ptr_t *)curr_node, depth, FALSE,
-                                               H5AC__NO_FLAGS_SET))) /* Casting away const OK -QAK */
+            (internal = H5B2__protect_internal(hdr, parent, curr_node, depth, FALSE, H5AC__NO_FLAGS_SET)))
             HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect B-tree internal node")
 
         /* Set up information about current node */
@@ -1824,7 +1822,7 @@ H5B2__delete_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_n
  *-------------------------------------------------------------------------
  */
 herr_t
-H5B2__node_size(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_node, void *parent,
+H5B2__node_size(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node, void *parent,
                 hsize_t *btree_size)
 {
     H5B2_internal_t *internal  = NULL;    /* Pointer to internal node */
@@ -1839,8 +1837,8 @@ H5B2__node_size(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_nod
     HDassert(depth > 0);
 
     /* Lock the current B-tree node */
-    if (NULL == (internal = H5B2__protect_internal(hdr, parent, (H5B2_node_ptr_t *)curr_node, depth, FALSE,
-                                                   H5AC__READ_ONLY_FLAG))) /* Casting away const OK -QAK */
+    if (NULL ==
+        (internal = H5B2__protect_internal(hdr, parent, curr_node, depth, FALSE, H5AC__READ_ONLY_FLAG)))
         HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect B-tree internal node")
 
     /* Recursively descend into child nodes, if we are above the "twig" level in the B-tree */
@@ -1910,7 +1908,7 @@ H5B2__create_flush_depend(H5AC_info_t *parent_entry, H5AC_info_t *child_entry)
  *-------------------------------------------------------------------------
  */
 herr_t
-H5B2__update_flush_depend(H5B2_hdr_t *hdr, unsigned depth, const H5B2_node_ptr_t *node_ptr, void *old_parent,
+H5B2__update_flush_depend(H5B2_hdr_t *hdr, unsigned depth, H5B2_node_ptr_t *node_ptr, void *old_parent,
                           void *new_parent)
 {
     const H5AC_class_t *child_class;           /* Pointer to child node's class info */
@@ -1941,9 +1939,8 @@ H5B2__update_flush_depend(H5B2_hdr_t *hdr, unsigned depth, const H5B2_node_ptr_t
             H5B2_internal_t *child_int;
 
             /* Protect child */
-            if (NULL == (child_int = H5B2__protect_internal(
-                             hdr, new_parent, (H5B2_node_ptr_t *)node_ptr, (uint16_t)(depth - 1), FALSE,
-                             H5AC__NO_FLAGS_SET))) /* Casting away const OK -QAK */
+            if (NULL == (child_int = H5B2__protect_internal(hdr, new_parent, node_ptr, (uint16_t)(depth - 1),
+                                                            FALSE, H5AC__NO_FLAGS_SET)))
                 HGOTO_ERROR(H5E_BTREE, H5E_CANTPROTECT, FAIL, "unable to protect B-tree internal node")
             child_class = H5AC_BT2_INT;
             child       = child_int;
@@ -2010,7 +2007,7 @@ H5B2__update_flush_depend(H5B2_hdr_t *hdr, unsigned depth, const H5B2_node_ptr_t
  *-------------------------------------------------------------------------
  */
 static herr_t
-H5B2__update_child_flush_depends(H5B2_hdr_t *hdr, unsigned depth, const H5B2_node_ptr_t *node_ptrs,
+H5B2__update_child_flush_depends(H5B2_hdr_t *hdr, unsigned depth, H5B2_node_ptr_t *node_ptrs,
                                  unsigned start_idx, unsigned end_idx, void *old_parent, void *new_parent)
 {
     unsigned u;                   /* Local index variable */

src/H5B2pkg.h

@@ -321,7 +321,7 @@ extern const H5B2_class_t *const H5B2_client_class_g[H5B2_NUM_BTREE_ID];
 
 /* Generic routines */
 H5_DLL herr_t H5B2__create_flush_depend(H5AC_info_t *parent_entry, H5AC_info_t *child_entry);
-H5_DLL herr_t H5B2__update_flush_depend(H5B2_hdr_t *hdr, unsigned depth, const H5B2_node_ptr_t *node_ptr,
+H5_DLL herr_t H5B2__update_flush_depend(H5B2_hdr_t *hdr, unsigned depth, H5B2_node_ptr_t *node_ptr,
                                         void *old_parent, void *new_parent);
 H5_DLL herr_t H5B2__destroy_flush_depend(H5AC_info_t *parent_entry, H5AC_info_t *child_entry);
 
@@ -390,9 +390,9 @@ H5_DLL herr_t H5B2__update_leaf(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_node_ptr,
                                 void *op_data);
 
 /* Routines for iterating over nodes/records */
-H5_DLL herr_t H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_node,
-                                 void *parent, H5B2_operator_t op, void *op_data);
-H5_DLL herr_t H5B2__node_size(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_node, void *parent,
+H5_DLL herr_t H5B2__iterate_node(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node, void *parent,
+                                 H5B2_operator_t op, void *op_data);
+H5_DLL herr_t H5B2__node_size(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node, void *parent,
                               hsize_t *op_data);
 
 /* Routines for locating records */
@@ -423,8 +423,8 @@ H5_DLL herr_t H5B2__remove_leaf_by_idx(H5B2_hdr_t *hdr, H5B2_node_ptr_t *curr_no
                                        void *op_data);
 
 /* Routines for deleting nodes */
-H5_DLL herr_t H5B2__delete_node(H5B2_hdr_t *hdr, uint16_t depth, const H5B2_node_ptr_t *curr_node,
-                                void *parent, H5B2_remove_t op, void *op_data);
+H5_DLL herr_t H5B2__delete_node(H5B2_hdr_t *hdr, uint16_t depth, H5B2_node_ptr_t *curr_node, void *parent,
+                                H5B2_remove_t op, void *op_data);
 
 /* Debugging routines for dumping file structures */
 H5_DLL herr_t H5B2__hdr_debug(H5F_t *f, haddr_t addr, FILE *stream, int indent, int fwidth,

src/H5Dchunk.c

@@ -5190,14 +5190,11 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_fill_info_t *chunk_
 static int
 H5D__chunk_cmp_coll_fill_info(const void *_entry1, const void *_entry2)
 {
-    const struct chunk_coll_fill_info *entry1;
-    const struct chunk_coll_fill_info *entry2;
+    const struct chunk_coll_fill_info *entry1 = (const struct chunk_coll_fill_info *)_entry1;
+    const struct chunk_coll_fill_info *entry2 = (const struct chunk_coll_fill_info *)_entry2;
 
     FUNC_ENTER_STATIC_NOERR
 
-    entry1 = (const struct chunk_coll_fill_info *)_entry1;
-    entry2 = (const struct chunk_coll_fill_info *)_entry2;
-
     FUNC_LEAVE_NOAPI(H5F_addr_cmp(entry1->addr, entry2->addr))
 } /* end H5D__chunk_cmp_coll_fill_info() */
 #endif /* H5_HAVE_PARALLEL */

src/H5Dmpio.c

@@ -2577,9 +2577,9 @@ H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_in
 {
     const H5D_filtered_collective_io_info_t *entry1;
     const H5D_filtered_collective_io_info_t *entry2;
-    haddr_t                                  addr1 = HADDR_UNDEF;
-    haddr_t                                  addr2 = HADDR_UNDEF;
-    int                                      ret_value;
+    haddr_t                                  addr1     = HADDR_UNDEF;
+    haddr_t                                  addr2     = HADDR_UNDEF;
+    int                                      ret_value = 0;
 
     FUNC_ENTER_STATIC_NOERR
 
@@ -2631,7 +2631,7 @@ H5D__cmp_chunk_redistribute_info(const void *_entry1, const void *_entry2)
     const H5D_chunk_redistribute_info_t *entry2;
     hsize_t                              chunk_index1;
     hsize_t                              chunk_index2;
-    int                                  ret_value;
+    int                                  ret_value = 0;
 
     FUNC_ENTER_STATIC_NOERR
 
@@ -2672,9 +2672,9 @@ H5D__cmp_chunk_redistribute_info_orig_owner(const void *_entry1, const void *_en
 {
     const H5D_chunk_redistribute_info_t *entry1;
     const H5D_chunk_redistribute_info_t *entry2;
-    int                                  owner1 = -1;
-    int                                  owner2 = -1;
-    int                                  ret_value;
+    int                                  owner1    = -1;
+    int                                  owner2    = -1;
+    int                                  ret_value = 0;
 
     FUNC_ENTER_STATIC_NOERR
 

src/H5FDhdfs.c

@@ -1730,7 +1730,7 @@ H5FD_hdfs_init(void)
 }
 
 herr_t
-H5Pget_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa_out)
+H5Pget_fapl_hdfs(hid_t H5_ATTR_UNUSED fapl_id, H5FD_hdfs_fapl_t H5_ATTR_UNUSED *fa_out)
 {
     herr_t ret_value = FAIL;
 
@@ -1744,7 +1744,7 @@ H5Pget_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa_out)
 }
 
 herr_t
-H5Pset_fapl_hdfs(hid_t fapl_id, H5FD_hdfs_fapl_t *fa)
+H5Pset_fapl_hdfs(hid_t H5_ATTR_UNUSED fapl_id, H5FD_hdfs_fapl_t H5_ATTR_UNUSED *fa)
 {
     herr_t ret_value = FAIL;
 

src/H5Gname.c

@@ -307,7 +307,7 @@ H5G__build_fullpath(const char *prefix, const char *name)
     /* Build full path */
     HDstrncpy(full_path, prefix, orig_path_len + 1);
     if (need_sep)
-        HDstrncat(full_path, "/", (size_t)1);
+        HDstrcat(full_path, "/");
     HDstrncat(full_path, name, name_len);
 
     /* Create reference counted string for path */

src/H5RS.c

@@ -174,8 +174,16 @@ H5RS_wrap(const char *s)
     if (NULL == (ret_value = H5FL_MALLOC(H5RS_str_t)))
         HGOTO_ERROR(H5E_RS, H5E_CANTALLOC, NULL, "memory allocation failed")
 
-    /* Set the internal fields */
-    ret_value->s       = (char *)s;
+    /* Set the internal fields
+     *
+     * We ignore warnings about storing a const char pointer in the struct
+     * since we never modify or free the string when the wrapped struct
+     * field is set to TRUE.
+     */
+    H5_GCC_DIAG_OFF("cast-qual")
+    ret_value->s = (char *)s;
+    H5_GCC_DIAG_ON("cast-qual")
+
     ret_value->wrapped = 1;
     ret_value->n       = 1;
 

src/H5Tref.c

@@ -709,6 +709,14 @@ H5T__ref_mem_write(H5VL_object_t *src_file, const void *src_buf, size_t src_size
  *
  *-------------------------------------------------------------------------
  */
+/*
+ * It is the correct thing to do to have the reference buffer
+ * be const-qualified here, but the VOL "blob specific" routine
+ * needs a non-const pointer since an operation might modify
+ * the "blob". Disable this warning here (at least temporarily)
+ * for this reason.
+ */
+H5_GCC_DIAG_OFF("cast-qual")
 static herr_t
 H5T__ref_disk_isnull(const H5VL_object_t *src_file, const void *src_buf, hbool_t *isnull)
 {
@@ -742,6 +750,7 @@ H5T__ref_disk_isnull(const H5VL_object_t *src_file, const void *src_buf, hbool_t
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5T__ref_disk_isnull() */
+H5_GCC_DIAG_ON("cast-qual")
 
 /*-------------------------------------------------------------------------
  * Function:    H5T__ref_disk_setnull

src/H5trace.c

@@ -120,8 +120,8 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
     void *            vp                  = NULL;
     FILE *            out                 = H5_debug_g.trace;
     static hbool_t    is_first_invocation = TRUE;
-    H5_timer_t        function_timer      = {{0}, {0}, {0}, FALSE};
-    H5_timevals_t     function_times;
+    H5_timer_t        function_timer;
+    H5_timevals_t     function_times = {0.0, 0.0, 0.0};
     static H5_timer_t running_timer;
     H5_timevals_t     running_times;
     static int        current_depth   = 0;
@@ -133,6 +133,10 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
         return 0.0F; /*tracing is off*/
     HDva_start(ap, type);
 
+    /* Initialize the timer for this function */
+    if (H5_debug_g.ttimes)
+        H5_timer_init(&function_timer);
+
     if (H5_debug_g.ttop) {
         if (returning) {
             if (current_depth > 1) {
@@ -156,11 +160,10 @@ H5_trace(const double *returning, const char *func, const char *type, ...)
         H5_timer_init(&running_timer);
         H5_timer_start(&running_timer);
     } /* end if */
-    if (H5_debug_g.ttimes) {
-        /* start the timer for this function */
-        H5_timer_init(&function_timer);
+
+    /* Start the timer for this function */
+    if (H5_debug_g.ttimes)
         H5_timer_start(&function_timer);
-    } /* end if */
 
     /* Print the first part of the line.  This is the indication of the
      * nesting depth followed by the function name and either start of

test/chunk_info.c

@@ -482,10 +482,10 @@ test_get_chunk_info_highest_v18(hid_t fapl)
     unsigned flt_msk      = 0;                            /* Filter mask */
     unsigned read_flt_msk = 0;                            /* Filter mask after direct read */
     int      fillvalue    = -1;                           /* Fill value */
-    int      aggression   = 9;                            /* Compression aggression setting */
     hsize_t  offset[2]    = {0, 0};                       /* Offset coordinates of a chunk */
 #ifdef H5_HAVE_FILTER_DEFLATE
-    const Bytef *z_src = (const Bytef *)(direct_buf);
+    int          aggression = 9; /* Compression aggression setting */
+    const Bytef *z_src      = (const Bytef *)(direct_buf);
     Bytef *      z_dst; /* Destination buffer */
     uLongf       z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(CHK_SIZE);
     uLong        z_src_nbytes = (uLong)CHK_SIZE;

test/trefstr.c

@@ -186,7 +186,7 @@ test_refstr_cmp(void)
     H5RS_str_t *rs1; /* Ref-counted string created */
     H5RS_str_t *rs2; /* Ref-counted string created */
     int         cmp; /* Comparison value */
-    size_t      len; /* Length of string */
+    ssize_t     len; /* Length of string */
     herr_t      ret; /* Generic return value */
 
     /* Output message about test being performed */

testpar/t_span_tree.c

@@ -35,6 +35,8 @@
 #include "H5private.h"
 #include "testphdf5.h"
 
+#define LOWER_DIM_SIZE_COMP_TEST__RUN_TEST__DEBUG 0
+
 static void coll_write_test(int chunk_factor);
 static void coll_read_test(void);
 
@@ -1431,8 +1433,7 @@ lower_dim_size_comp_test__verify_data(uint32_t *buf_ptr,
  *-------------------------------------------------------------------------
  */
 
-#define LDSCT_DS_RANK                             5
-#define LOWER_DIM_SIZE_COMP_TEST__RUN_TEST__DEBUG 0
+#define LDSCT_DS_RANK 5
 
 static void
 lower_dim_size_comp_test__run_test(const int chunk_edge_size, const hbool_t use_collective_io,

tools/lib/h5diff_array.c

@@ -1597,6 +1597,9 @@ 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);