[Bug middle-end/49277] New: [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[Bug middle-end/49277] New: [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[hjl.tools at gmail dot com]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

           Summary: [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to
                    build
           Product: gcc
           Version: 4.7.0
            Status: UNCONFIRMED
          Severity: normal
          Priority: P3
         Component: middle-end
        AssignedTo: unassigned@gcc.gnu.org
        ReportedBy: hjl.tools@gmail.com


On Linux/ia32, revision 174523 gave

gcc -m32  -O2 -msse2 -mfpmath=sse -ffast-math -fwhole-program -flto=jobserver
-fuse-linker-plugin       -lm   alphabet.o core_algorithms.o debug.o display.o
emit.o emulation.o fast_algorithms.o histogram.o hmmio.o hmmcalibrate.o
hmmsearch.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o
postprob.o prior.o tophits.o trace.o ucbqsort.o a2m.o aligneval.o alignio.o
clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o
iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o
sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o
ssi.o stack.o stockholm.o translate.o types.o vectorops.o weight.o            
-lm        -o hmmer
...
In file included from :28:0:
hmmsearch.c: In function 'main_loop_serial':
hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4124_585 == 6)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4124_597 == 6)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4118_602 == 7)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4124_645 == 7)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4163_684 == 1)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4163_684 == 3)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4288_847 == 1)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4288_875 == 1)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4510_1347 == 59)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4510_1353 != 59)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4523_1394 == 0)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4550_1404 != 62)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4560_1447 == 45)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4560_1447 != 0)

hmmsearch.c:598:1: internal compiler error: verify_gimple failed
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://gcc.gnu.org/bugs.html> for instructions.
make[4]: *** [/tmp/ccGI9oyK.ltrans0.ltrans.o] Error 1
lto-wrapper: make returned 2 exit status
/usr/local/bin/ld: lto-wrapper failed
collect2: error: ld returned 1 exit status
specmake[3]: *** [hmmer] Error 1

[Bug lto/49277] [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[hjl.tools at gmail dot com]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

H.J. Lu <hjl.tools at gmail dot com> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |rguenth at gcc dot gnu.org
          Component|middle-end                  |lto

--- Comment #1 from H.J. Lu <hjl.tools at gmail dot com> 2011-06-03 14:40:05 UTC ---
It is caused by revision 174519:

http://gcc.gnu.org/ml/gcc-cvs/2011-06/msg00005.html

[Bug lto/49277] [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[rguenth at gcc dot gnu.org]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

Richard Guenther <rguenth at gcc dot gnu.org> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|UNCONFIRMED                 |ASSIGNED
   Last reconfirmed|                            |2011.06.06 08:47:54
   Target Milestone|---                         |4.7.0
     Ever Confirmed|0                           |1

--- Comment #2 from Richard Guenther <rguenth at gcc dot gnu.org> 2011-06-06 08:47:54 UTC ---
Mine.

[Bug lto/49277] [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[rguenth at gcc dot gnu.org]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

Richard Guenther <rguenth at gcc dot gnu.org> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |WAITING

--- Comment #3 from Richard Guenther <rguenth at gcc dot gnu.org> 2011-06-06 15:23:47 UTC ---
Works for me.

/abuild/rguenther/install/usr/local/bin/gcc   -m32 -msse2 -mfpmath=sse -O2
-ffast-math -fwhole-program -fuse-linker-plugin
-Wl,-rpath=/abuild/rguenther/install/usr/local/lib -flto=6          alphabet.o
core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o
histogram.o hmmio.o hmmcalibrate.o hmmsearch.o mathsupport.o masks.o misc.o
modelmakers.o plan7.o plan9.o postprob.o prior.o tophits.o trace.o ucbqsort.o
a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o
gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o
seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o
sre_random.o sre_string.o ssi.o stack.o stockholm.o translate.o types.o
vectorops.o weight.o             -lm        -o hmmer
/usr/bin/ld: Warning: alignment 4 of symbol `Alphabet' in
/tmp/ccb1HVsX.ltrans17.ltrans.o is smaller than 16 in hmmsearch.o.ironly
specmake -j6 options 2> options.err | tee options.out
...

Please provide a testcase.

[Bug lto/49277] [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[hjl.tools at gmail dot com]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

H.J. Lu <hjl.tools at gmail dot com> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|WAITING                     |NEW

--- Comment #4 from H.J. Lu <hjl.tools at gmail dot com> 2011-06-06 22:15:34 UTC ---
It depends on the glibc header files.  This testcase:

http://www.kernel.org/pub/linux/devel/gcc/lto/pr49277.tar.bz2

gave me:

/export/build/gnu/gcc/build-x86_64-linux/gcc/xgcc
-B/export/build/gnu/gcc/build-x86_64-linux/gcc/ -m32 -O2 -msse2 -mfpmath=sse
-ffast-math -DSPEC_CPU -DNDEBUG -fwhole-program -flto=jobserver
-fuse-linker-plugin -o hmmer alphabet.o core_algorithms.o debug.o display.o
emit.o emulation.o fast_algorithms.o histogram.o hmmio.o hmmcalibrate.o
hmmsearch.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o
postprob.o prior.o tophits.o trace.o ucbqsort.o a2m.o aligneval.o alignio.o
clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o
iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o
sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o
ssi.o stack.o stockholm.o translate.o types.o vectorops.o weight.o      -lm
In file included from :28:0:
hmmsearch.c: In function ‘main_loop_serial’:
hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4124_585 == 6)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4124_597 == 6)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4118_602 == 7)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4124_645 == 7)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4163_684 == 1)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4163_684 == 3)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4288_847 == 1)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4288_875 == 1)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4510_1347 == 59)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4510_1353 != 59)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4523_1394 == 0)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4550_1404 != 62)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4560_1447 == 45)

hmmsearch.c:598:1: error: type mismatch in comparison expression
bool
char
unsigned char
if (D.4560_1447 != 0)

hmmsearch.c:598:1: internal compiler error: verify_gimple failed
Please submit a full bug report,
with preprocessed source if appropriate.
See <http://gcc.gnu.org/bugs.html> for instructions.
make[1]: *** [/tmp/ccuQB7dT.ltrans0.ltrans.o] Error 1
lto-wrapper: make returned 2 exit status
/usr/local/bin/ld: lto-wrapper failed
collect2: error: ld returned 1 exit status
make: *** [hmmer] Error 1
[hjl@gnu-33 pr49277]$

[Bug lto/49277] [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[rguenther at suse dot de]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

--- Comment #5 from rguenther at suse dot de <rguenther at suse dot de> 2011-06-07 09:00:06 UTC ---
On Mon, 6 Jun 2011, hjl.tools at gmail dot com wrote:

> http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277
> 
> H.J. Lu <hjl.tools at gmail dot com> changed:
> 
>            What    |Removed                     |Added
> ----------------------------------------------------------------------------
>              Status|WAITING                     |NEW
> 
> --- Comment #4 from H.J. Lu <hjl.tools at gmail dot com> 2011-06-06 22:15:34 UTC ---
> It depends on the glibc header files.  This testcase:
> 
> http://www.kernel.org/pub/linux/devel/gcc/lto/pr49277.tar.bz2

Can you bisect the set of object files (adding -r -nostdlib to the link)
and provide preprocessed source for the minimal set of object files that
trigger at least one such error?

The object files are not compatible with the three versions of lto1
I have around.

It looks like a bug in some optimization pass (at least I didn't see
hmmer mixing -f[un]signed-char which would make my patch suspicious).

Thanks.

[Bug lto/49277] [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[hjl.tools at gmail dot com]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

--- Comment #6 from H.J. Lu <hjl.tools at gmail dot com> 2011-06-07 15:01:48 UTC ---
(In reply to comment #5)
> On Mon, 6 Jun 2011, hjl.tools at gmail dot com wrote:

> 
> Can you bisect the set of object files (adding -r -nostdlib to the link)
> and provide preprocessed source for the minimal set of object files that
> trigger at least one such error?

I will do that.

> The object files are not compatible with the three versions of lto1
> I have around.
> 

Which revision of GCC are you using? My testcase was compiled by
revision 174710.  I can build my testcase with the same revision of
your GCCs.

[Bug lto/49277] [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[rguenther at suse dot de]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

--- Comment #7 from rguenther at suse dot de <rguenther at suse dot de> 2011-06-07 15:20:37 UTC ---
On Tue, 7 Jun 2011, hjl.tools at gmail dot com wrote:

> http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277
> 
> --- Comment #6 from H.J. Lu <hjl.tools at gmail dot com> 2011-06-07 15:01:48 UTC ---
> (In reply to comment #5)
> > On Mon, 6 Jun 2011, hjl.tools at gmail dot com wrote:
> 
> > 
> > Can you bisect the set of object files (adding -r -nostdlib to the link)
> > and provide preprocessed source for the minimal set of object files that
> > trigger at least one such error?
> 
> I will do that.
> 
> > The object files are not compatible with the three versions of lto1
> > I have around.
> > 
> 
> Which revision of GCC are you using? My testcase was compiled by
> revision 174710.  I can build my testcase with the same revision of
> your GCCs.

preprocessed source is prefered, otherwise it's hard to minimize
the testcase further.

Richard.

[Bug lto/49277] [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[hjl.tools at gmail dot com]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

--- Comment #8 from H.J. Lu <hjl.tools at gmail dot com> 2011-06-07 22:29:21 UTC ---
It may be a pilot error.

[Bug lto/49277] [4.7 Regression] 456.hmmer in SPEC CPU 2006 failed to build

[hjl.tools at gmail dot com]

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49277

H.J. Lu <hjl.tools at gmail dot com> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |WORKSFORME

--- Comment #9 from H.J. Lu <hjl.tools at gmail dot com> 2011-06-08 05:08:20 UTC ---
I need to add -funsigned-char for final link.