-f[no-]builtin-* is a frontend option not supported by LTO (nor by Fortran
for example).  That it controls also middle-end behavior with respect to
LTO streaming 'pow' as a builtin is a bug I suppose (to be analyzed).
Probably caused by

      /* For variables prefer the builtin if one is available.  */
      else if (TREE_CODE (prevailing->symbol.decl) == FUNCTION_DECL)
        {
          for (e = first; e; e = e->symbol.next_sharing_asm_name)
            if (TREE_CODE (e->symbol.decl) == FUNCTION_DECL
                && DECL_BUILT_IN (e->symbol.decl))
              {
                prevailing = e;
                break;
              }
        }

and LTO un-conditionally initializing all builtins (well, and that's needed
unless we can do that lazily during streaming as we stream builtin decls
by their DECL_FUNCTION_CODE ...).

Hm.  I'll have a looksee.

Created attachment 29328 [details]
patch

We do stream things properly as / not as builtin.  Only we end up replacing
the non-builtin with the prevailing builtin.  It seems to me builtins should
never "prevail" (we do not touch their cgraph nodes either) but we also
should not replace any builtin decl with whatever prevailed (unless maybe
there is a visible definition ...?)

I have a patch but that causes PR55848 to re-appear (also in this testcase):

lto1: error: edge points to wrong declaration:^M
 <function_decl 0x7fb56f8d2a00 pow^M
    type <function_type 0x7fb56f8d1e70^M
...
 Instead of: <function_decl 0x7fb56f7e6f00 __builtin_pow^M
    type <function_type 0x7fb56f7b60a8^M

doesn't happen with -flto-partition=none though.  At LTRANs we again see

  d2_5 = __builtin_pow (d1_3, 3.33333333333333314829616256247390992939472198486328125e-1);
  d3_6 = __builtin_pow (d1_3, 2.0e+0);

which is of course wrong.  Something assumes there is only a single
prevailing cgraph node per symbol?  The callgraph at LTRANS time
looks ok to me:

pow/2 (pow) @0x7f5806f3ca68
  Type: function
  Visibility: undef external public
  previous sharing asm name: 3
  References:
  Referring:
  Read from file: /tmp/ccp4tasf.ltrans0.o
  Function flags:
  Called by: main/1 (1.00 per call)
  Calls:
pow/3 (__builtin_pow) @0x7f5806f3c940
  Type: function
  Visibility: external public
  next sharing asm name: 2
  References:
  Referring:
  Read from file: /tmp/ccp4tasf.ltrans0.o
  Function flags:
  Called by: main/1 (1.00 per call)
main/1 (main) @0x7f5806f3c6f0
  Type: function
  Visibility: prevailing_def public
  References: x.2385/0 (read)
  Referring:
  Read from file: /tmp/ccp4tasf.ltrans0.o
  Function flags: analyzed finalized only_called_at_startup
  Called by:
  Calls: abort/4 (0.39 per call) pow/3 (1.00 per call) pow/2 (1.00 per call)

but then somehow it's all wrong when reading the call op of the call stmt.
The ltrans object fn decl state stream of main has both a builtin and
a non-builtin.  That's because LTRANS thinks the builtin prevailed.  Bah.
That's because it happens to come "first" and we skip lto_symtab_merge_decls
for LTRANS.  Probably ok, but then we also should skip lto_fixup_decls.

Created attachment 29329 [details]
alternative patch

Patch which disables fixup_decls in LTRANS mode (fixes the testcase).  Trying
that on LTO bootstrap now ...

Author: rguenth
Date: Mon Feb  4 12:19:25 2013
New Revision: 195709

URL: http://gcc.gnu.org/viewcvs?root=gcc&view=rev&rev=195709
Log:
2013-02-04  Richard Guenther  <rguenther@suse.de>

	PR lto/56168
	* lto-symtab.c (lto_symtab_merge_decls_1): Make non-builtin
	node prevail as last resort.
	(lto_symtab_merge_decls): Remove guard on LTRANS here.
	(lto_symtab_prevailing_decl): Builtins are their own prevailing
	decl.

	lto/
	* lto.c (read_cgraph_and_symbols): Do not call lto_symtab_merge_decls
	or lto_fixup_decls at LTRANS time.

	* gcc.dg/lto/pr56168_0.c: New testcase.
	* gcc.dg/lto/pr56168_1.c: Likewise.

Added:
    trunk/gcc/testsuite/gcc.dg/lto/pr56168_0.c
    trunk/gcc/testsuite/gcc.dg/lto/pr56168_1.c
Modified:
    trunk/gcc/ChangeLog
    trunk/gcc/lto-symtab.c
    trunk/gcc/lto/ChangeLog
    trunk/gcc/lto/lto.c
    trunk/gcc/testsuite/ChangeLog

Fixed.