Hi,
this patch adjusts LTO tree merging to treat anonymous namespace types
as local to a given TU, so just like !TREE_PUBLIC decls they are not
merged (this is unify_scc change). This makes them to get different
canonical types and act as independent types for TBAA.

I also modified canonical type calculation to never consider anonymous
namespace types as interoperable with structurally equivalent types
declared in non-C++ translation units.

Both these changes are tested by the testcase (first change makes set1
and set2 independent and second chnage makes set1&set2 independent of
set3).

lto-bootstrapped/regtested x86_64-linux
Honza

        * lto-common.c (gimple_register_canonical_type_1): Do not look for
        non-ODR conflicts of types in anonymous namespaces.
        (unify_scc): Do not merge anonymous namespace types.
        * g++.dg/lto/alias-5_0.C: New testcase.
        * g++.dg/lto/alias-5_1.C: New.
        * g++.dg/lto/alias-5_2.c: New.
Index: lto/lto-common.c
===================================================================
--- lto/lto-common.c    (revision 273551)
+++ lto/lto-common.c    (working copy)
@@ -418,13 +418,19 @@ gimple_register_canonical_type_1 (tree t
   if (RECORD_OR_UNION_TYPE_P (t)
       && odr_type_p (t) && !odr_type_violation_reported_p (t))
     {
-      /* Here we rely on fact that all non-ODR types was inserted into
-        canonical type hash and thus we can safely detect conflicts between
-        ODR types and interoperable non-ODR types.  */
-      gcc_checking_assert (type_streaming_finished
-                          && TYPE_MAIN_VARIANT (t) == t);
-      slot = htab_find_slot_with_hash (gimple_canonical_types, t, hash,
-                                      NO_INSERT);
+      /* Anonymous namespace types never conflict with non-C++ types.  */
+      if (type_with_linkage_p (t) && type_in_anonymous_namespace_p (t))
+       slot = NULL;
+      else
+       {
+         /* Here we rely on fact that all non-ODR types was inserted into
+            canonical type hash and thus we can safely detect conflicts between
+            ODR types and interoperable non-ODR types.  */
+         gcc_checking_assert (type_streaming_finished
+                              && TYPE_MAIN_VARIANT (t) == t);
+         slot = htab_find_slot_with_hash (gimple_canonical_types, t, hash,
+                                          NO_INSERT);
+       }
       if (slot && !TYPE_CXX_ODR_P (*(tree *)slot))
        {
          tree nonodr = *(tree *)slot;
@@ -1640,11 +1646,14 @@ unify_scc (class data_in *data_in, unsig
       tree t = streamer_tree_cache_get_tree (cache, from + i);
       scc->entries[i] = t;
       /* Do not merge SCCs with local entities inside them.  Also do
-        not merge TRANSLATION_UNIT_DECLs.  */
+        not merge TRANSLATION_UNIT_DECLs and anonymous namespace types.  */
       if (TREE_CODE (t) == TRANSLATION_UNIT_DECL
          || (VAR_OR_FUNCTION_DECL_P (t)
              && !(TREE_PUBLIC (t) || DECL_EXTERNAL (t)))
-         || TREE_CODE (t) == LABEL_DECL)
+         || TREE_CODE (t) == LABEL_DECL
+         || (TYPE_P (t)
+             && type_with_linkage_p (TYPE_MAIN_VARIANT (t))
+             && type_in_anonymous_namespace_p (TYPE_MAIN_VARIANT (t))))
        {
          /* Avoid doing any work for these cases and do not worry to
             record the SCCs for further merging.  */
Index: testsuite/g++.dg/lto/alias-5_0.C
===================================================================
--- testsuite/g++.dg/lto/alias-5_0.C    (nonexistent)
+++ testsuite/g++.dg/lto/alias-5_0.C    (working copy)
@@ -0,0 +1,35 @@
+/* { dg-lto-do run } */
+/* { dg-lto-options { { -O3 -flto } } } */
+/* This testcase tests that anonymous namespaces in different TUs are treated
+   as different types by LTO TBAA and that they never alias with structurally
+   same C types.  */
+namespace {
+  __attribute__((used))
+  struct a {int a;} *p,**ptr=&p;
+};
+void
+set1()
+{
+  *ptr=0;
+}
+void
+get1()
+{
+  if (!__builtin_constant_p (*ptr==0))
+    __builtin_abort ();
+}
+extern void set2();
+extern "C" void set3();
+int n = 1;
+int
+main()
+{
+  for (int i = 0; i < n; i++)
+    {
+      set1();
+      set2();
+      set3();
+      get1();
+    }
+  return 0;
+}
Index: testsuite/g++.dg/lto/alias-5_1.C
===================================================================
--- testsuite/g++.dg/lto/alias-5_1.C    (nonexistent)
+++ testsuite/g++.dg/lto/alias-5_1.C    (working copy)
@@ -0,0 +1,9 @@
+namespace {
+  __attribute__((used))
+  struct a {int a;} *p,**ptr=&p,q;
+};
+void
+set2()
+{
+  *ptr=&q;
+}
Index: testsuite/g++.dg/lto/alias-5_2.c
===================================================================
--- testsuite/g++.dg/lto/alias-5_2.c    (nonexistent)
+++ testsuite/g++.dg/lto/alias-5_2.c    (working copy)
@@ -0,0 +1,7 @@
+  __attribute__((used))
+  struct a {int a;} *p,**ptr=&p,q;
+void
+set3()
+{
+  *ptr=&q;
+}

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