[Bug fortran/26106] New: Gfortran can't compile tonto

[Bug fortran/26106] New: Gfortran can't compile tonto

[hjl at lucon dot org]

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I tried to compile the TONTO_1_0_SPEC branch of Tonto:

http://sourceforge.net/projects/tonto-chem

I got

/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/shell1.o f95files/shell1.F90
f95files/shell1.F90: In function âprocess_keywordâ:
f95files/shell1.F90:571: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://gcc.gnu.org/bugs.html> for instructions.

/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/spacegroup.o f95files/spacegroup.F90
f95files/spacegroup.F90: In function âput_matching_hm_symbolsâ:
f95files/spacegroup.F90:2455: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://gcc.gnu.org/bugs.html> for instructions.

/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/scfdata.o f95files/scfdata.F90
f95files/scfdata.F90: In function âprocess_keywordâ:
f95files/scfdata.F90:972: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://gcc.gnu.org/bugs.html> for instructions.

/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/mol_main.o f95files/mol_main.F90
f95files/mol_main.F90: In function âprocess_keywordâ:
f95files/mol_main.F90:3835: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://gcc.gnu.org/bugs.html> for instructions.

/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/mol.o f95files/mol.F90
f95files/mol.F90: In function âput_scf_energy_in_mo_pairsâ:
f95files/mol.F90:14792: fatal error: gfc_todo: Not Implemented: Scalarization
of non-elemental intrinsic: __transfer1
compilation terminated.


-- 
           Summary: Gfortran can't compile tonto
           Product: gcc
           Version: 4.2.0
            Status: UNCONFIRMED
          Keywords: meta-bug
          Severity: normal
          Priority: P3
         Component: fortran
        AssignedTo: unassigned at gcc dot gnu dot org
        ReportedBy: hjl at lucon dot org


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[pinskia at gcc dot gnu dot org]

------- Comment #1 from pinskia at gcc dot gnu dot org  2006-02-05 16:41 -------
PR 17298 is for __transfer1 TODO


-- 

pinskia at gcc dot gnu dot org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
  BugsThisDependsOn|                            |17298
            Summary|Gfortran can't compile tonto|[meta-bug] Gfortran can't
                   |                            |compile tonto


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[pinskia at gcc dot gnu dot org]

-- 

pinskia at gcc dot gnu dot org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
  BugsThisDependsOn|                            |26038, 26041
             Status|UNCONFIRMED                 |NEW
     Ever Confirmed|0                           |1
   Last reconfirmed|0000-00-00 00:00:00         |2006-02-05 17:37:25
               date|                            |


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[kargl at gcc dot gnu dot org]

------- Comment #2 from kargl at gcc dot gnu dot org  2006-03-11 19:27 -------
I can't reproduce any of these failures (except for __transfer1).
HJ, can you at least attached the preprocessed code?


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[hjl at lucon dot org]

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------- Comment #3 from hjl at lucon dot org  2006-03-11 20:15 -------
I don't know how to preprocess Fortran code. I still see those failures with

gcc version 4.2.0 20060311 (experimental) [trunk revision 111963 clean]

on Linux/x86-64. For example:

[hjl@gnu-13 tonto]$ /usr/gcc-4.2/bin/gfortran  -I.
-I./GCC-gfortran-on-LINUX/modules -O -c  f95files/shell1.F90
f95files/shell1.F90: In function âprocess_keywordâ:
f95files/shell1.F90:571: internal compiler error: Segmentation fault
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://gcc.gnu.org/bugs.html> for instructions.

I tried

[hjl@gnu-13 tonto]$ /usr/gcc-4.2/bin/gfortran -c -O shell.f90
 In file f95files/shell1.F90:29

   use TYPES_MODULE
                  1
Fatal Error: Can't open module file 'types_module.mod' for reading at (1): No
such file or directory
[hjl@gnu-13 tonto]$

Can you show your output of compiling f95files/shell1.F90?

BTW, I need this patch

--- tonto/Makefile.pl.gcc       2006-02-05 07:47:12.000000000 -0800
+++ tonto/Makefile.pl   2006-02-05 08:02:03.000000000 -0800
@@ -41,6 +41,7 @@ my %vendors = (
 'PGI'        => 'Portland',
 'INTEL'      => 'Intel',
 'ABSOFT'     => 'Absoft',
+'GCC'        => 'gcc',
 );


################################################################################

to configure tonto for gcc 4.2.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[pault at gcc dot gnu dot org]

------- Comment #4 from pault at gcc dot gnu dot org  2006-03-15 16:53 -------
You will be glad to hear that, at long last, I am putting the finishing touches
to a patch for transfer.  It needs comments and a fine-toothed combing of the
code.  I maybe will submit it tomorrow morning.

Paul Thomas


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[kargl at gcc dot gnu dot org]

------- Comment #5 from kargl at gcc dot gnu dot org  2006-03-15 17:26 -------
(In reply to comment #4)
> You will be glad to hear that, at long last, I am putting the finishing touches
> to a patch for transfer.  It needs comments and a fine-toothed combing of the
> code.  I maybe will submit it tomorrow morning.

This won't help compiling tonto-chem.  AFAICT, this code is
riddled with nonstandard code.  I can't compile it with either
gfortran or NAG's F95 compiler.  Additionally, it's rather
odd build infrastructure makes it hard to follow what's going on.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[hjl at lucon dot org]

------- Comment #6 from hjl at lucon dot org  2006-03-15 19:31 -------
Please point out the non-standard code in tonto in detail. I will report it to
our SPEC people.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[kargl at gcc dot gnu dot org]

------- Comment #7 from kargl at gcc dot gnu dot org  2006-03-15 20:01 -------
(In reply to comment #6)
> Please point out the non-standard code in tonto in detail. I will report it to
> our SPEC people.
> 

I believe that the code associated with gfortran's error message
is nonstandard at least with respect to Fortran 95 and earlier.

Making UNKNOWN-gfc4x-on-FREEBSD/modules/vec_int_module.mod ...
Target ./UNKNOWN-gfc4x-on-FREEBSD/modules/vec_int_module.mod does not exist,
compilation forced.
set noglob && /mnt1/sgk/bin/gfc4x -I. -I./UNKNOWN-gfc4x-on-FREEBSD/modules -O
-c -o ./UNKNOWN-gfc4x-on-FREEBSD/objects/vec\{int}.o
UNKNOWN-gfc4x-on-FREEBSD/f95files/vec\{int}.F90
 In file UNKNOWN-gfc4x-on-FREEBSD/f95files/vec{int}.F90:804

      integer(4), dimension(n_elements_uncommon_with_(self,v)) :: res
                           1
Error: Expression at (1) must be of INTEGER type


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[hjl at lucon dot org]

------- Comment #8 from hjl at lucon dot org  2006-03-15 20:18 -------
Is that the exact output? I couldn't find similar thing in my log. The
closest things I have are

/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/intvec.o f95files/intvec.F90
/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/intvecvec.o f95files/intvecvec.F90
/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/intvecintvechash.o
f95files/intvecintvechash.F90
/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/intvecmat3.o f95files/intvecmat3.F90


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[kargl at gcc dot gnu dot org]

------- Comment #9 from kargl at gcc dot gnu dot org  2006-03-15 20:42 -------
(In reply to comment #8)
> Is that the exact output?

Yes, of course!


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[hjl at lucon dot org]

------- Comment #10 from hjl at lucon dot org  2006-03-15 23:28 -------
(In reply to comment #9)
> (In reply to comment #8)
> > Is that the exact output?
> 
> Yes, of course!
> 

I assum you tried to compile f95files/intvec.F90. I have no problem with it:

[hjl@gnu-13 tonto]$ perl Makefile.pl --fc=/usr/gcc-4.2/bin/gfortran
Getting operating system name ... LINUX
Checking for perl ... /usr/bin/perl
Checking for make ... /usr/bin/gmake
Checking whether GNU make ... yes
Checking for Fortran compiler ... /usr/gcc-4.2/bin/gfortran

Determining Fortran compiler vendor ... GCC
Options for your compiler are in ./site_config/GCC-gfortran-on-LINUX

[hjl@gnu-13 tonto]$ make
...
/usr/gcc-4.2/bin/gfortran -I. -I./GCC-gfortran-on-LINUX/modules -O -c -o
./GCC-gfortran-on-LINUX/objects/intvec.o f95files/intvec.F90
...

[hjl@gnu-13 tonto]$ ls -l ./GCC-gfortran-on-LINUX/objects/intvec.o
-rw-rw-r--  1 hjl hjl 55408 Mar 15 14:03
./GCC-gfortran-on-LINUX/objects/intvec.o


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

Re: [Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[Andrew Pinski]

On Mar 15, 2006, at 6:28 PM, hjl at lucon dot org wrote:

>
>
> ------- Comment #10 from hjl at lucon dot org  2006-03-15 23:28 -------
> (In reply to comment #9)
>> (In reply to comment #8)
>>> Is that the exact output?
>>
>> Yes, of course!
>>
>
> I assum you tried to compile f95files/intvec.F90. I have no problem 
> with it:

Maybe the SPEC branch has it already fixed but the mainline of TONTO 
does not.

-- Pinski

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[pinskia at physics dot uc dot edu]

------- Comment #11 from pinskia at gcc dot gnu dot org  2006-03-15 23:33 -------
Subject: Re:  [meta-bug] Gfortran can't compile tonto


On Mar 15, 2006, at 6:28 PM, hjl at lucon dot org wrote:

>
>
> ------- Comment #10 from hjl at lucon dot org  2006-03-15 23:28 -------
> (In reply to comment #9)
>> (In reply to comment #8)
>>> Is that the exact output?
>>
>> Yes, of course!
>>
>
> I assum you tried to compile f95files/intvec.F90. I have no problem 
> with it:

Maybe the SPEC branch has it already fixed but the mainline of TONTO 
does not.

-- Pinski


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[hjl at lucon dot org]

------- Comment #12 from hjl at lucon dot org  2006-03-16 00:14 -------
I(In reply to comment #11)
> Subject: Re:  [meta-bug] Gfortran can't compile tonto
> 
> 
> On Mar 15, 2006, at 6:28 PM, hjl at lucon dot org wrote:
> 
> >
> >
> > ------- Comment #10 from hjl at lucon dot org  2006-03-15 23:28 -------
> > (In reply to comment #9)
> >> (In reply to comment #8)
> >>> Is that the exact output?
> >>
> >> Yes, of course!
> >>
> >
> > I assum you tried to compile f95files/intvec.F90. I have no problem 
> > with it:
> 
> Maybe the SPEC branch has it already fixed but the mainline of TONTO 
> does not.
> 
> -- Pinski
> 

I did say:

I tried to compile the TONTO_1_0_SPEC branch of Tonto:

http://sourceforge.net/projects/tonto-chem

...


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[pinskia at gcc dot gnu dot org]

------- Comment #13 from pinskia at gcc dot gnu dot org  2006-03-16 05:08 -------
PR23634 does not affect this PR.  So only two bugs left.  I checked by
commenting out the lines effecting compiling.


-- 

pinskia at gcc dot gnu dot org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
  BugsThisDependsOn|23634                       |


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[paul dot richard dot thomas at cea dot fr]

------- Comment #14 from paul dot richard dot thomas at cea dot fr  2006-04-10 15:07 -------
(In reply to comment #13)
> PR23634 does not affect this PR.  So only two bugs left.  I checked by
> commenting out the lines effecting compiling.

I have submitted 2 PRs for tonto-2.2; PR25597 and PR27096.

The first I have submitted a patch for and the patch for the second will be
submitted tonight.

Paul


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[paul dot richard dot thomas at cea dot fr]

------- Comment #15 from paul dot richard dot thomas at cea dot fr  2006-04-13 13:36 -------
I can now compile tonto-1.0 without any kludges or tricks.  That said, it
segfaults immediately after reading the input data.  I will endeavour to find
the cause.

tonto-2.x is blocked by complex(ie. complicated) constructors, which in the
words of "Hitch-hikers Guide to the Galaxy", "will take a little while";
although I hope to improve on the 4 million years of the story....

Paul


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[hjl at lucon dot org]

------- Comment #16 from hjl at lucon dot org  2006-04-13 13:48 -------
Created an attachment (id=11257)
 --> (http://gcc.gnu.org/bugzilla/attachment.cgi?id=11257&action=view)
A patch to nullify pointers in local variables

Tonto 1.0 has many local variables with uninitialized pointers. This patch
fixes them.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[hjl at lucon dot org]

------- Comment #17 from hjl at lucon dot org  2006-04-13 13:49 -------
Created an attachment (id=11258)
 --> (http://gcc.gnu.org/bugzilla/attachment.cgi?id=11258&action=view)
Another patch

This is another patch to initialize local variable and fix a typo.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[pault at gcc dot gnu dot org]

------- Comment #18 from pault at gcc dot gnu dot org  2006-04-19 04:59 -------
(In reply to comment #15)
> I can now compile tonto-1.0 without any kludges or tricks.  That said, it
> segfaults immediately after reading the input data.  I will endeavour to find
> the cause.

This happens in a call to intrinsic flush, during the initial input.

> 
> tonto-2.x is blocked by complex(ie. complicated) constructors, which in the
> words of "Hitch-hikers Guide to the Galaxy", "will take a little while";
> although I hope to improve on the 4 million years of the story....
> 
> Paul
> 

Please see yesterday's submission of a patch for this:
http://gcc.gnu.org/ml/fortran/2006-04/msg00221.html

Paul


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[jvdelisle at gcc dot gnu dot org]

------- Comment #19 from jvdelisle at gcc dot gnu dot org  2006-04-20 06:21 -------
Created an attachment (id=11300)
 --> (http://gcc.gnu.org/bugzilla/attachment.cgi?id=11300&action=view)
tonto-1.0 input file stdin.h.uhf

With this attachment as input I get a successful output with tonto-1.0.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[jvdelisle at gcc dot gnu dot org]

------- Comment #20 from jvdelisle at gcc dot gnu dot org  2006-04-20 06:25 -------
Created an attachment (id=11301)
 --> (http://gcc.gnu.org/bugzilla/attachment.cgi?id=11301&action=view)
tonto-1.0 output for stdin.h.uhf

Here is the output from the above patch.  When I go to stdin.h2o.blyp I get a
segfault.  Valgrind is showing unitialized values being used.  I am not using
the spec version of tonto. I am using the 1.0 download from sourceforge.

An added note, when attempting to compile tonto with the -g option I got an ice
related to transfer.  I will have to take another look later and report back
here.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto

[jvdelisle at gcc dot gnu dot org]

------- Comment #21 from jvdelisle at gcc dot gnu dot org  2006-04-22 04:48 -------
I am able to compile with -g OK.  Not sure what I was seeing the other night.

Here is a backtrace where I see a segfault:

(gdb) bt
#0  0x082c1c15 in __atom_module__n_bf (self=@0xa2908a8) at
f95files/atom.F90:2251
#1  0x082cb859 in __atomvec_module__n_bf (self=@0xa28fef8)
    at f95files/atomvec.F90:4147
#2  0x081296ae in __mol_module__set_basis_info (self=@0xa28fe28)
    at f95files/mol.F90:3473
#3  0x0812a519 in __mol_module__resolve_gaussianbasis_info (self=@0xa28fe28)
    at f95files/mol.F90:3355
#4  0x0812a5e0 in __mol_module__resolve_basis_info (self=@0xa28fe28)
    at f95files/mol.F90:3290
#5  0x080d5dd6 in __mol_module__read_atoms (self=@0xa28fe28)
    at f95files/mol.F90:9587
#6  0x0804e79d in __mol_main_module__process_keyword (self=@0x8513064,
    keyword=@0xbfaa5324, _keyword=128) at f95files/mol_main.F90:3844
#7  0x08050e13 in __mol_main_module__read_keywords (self=@0x8513064)
    at f95files/mol_main.F90:3815
#8  0x08051341 in __mol_main_module__main (self=@0x8513064)
    at f95files/mol_main.F90:3753
#9  0x08049a3c in MAIN__ () at f95files/run_mol.F90:134
#10 0x084a0ef7 in main (argc=Cannot access memory at address 0x3
) at ../../../main/libgfortran/fmain.c:18


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto correctly

[hjl at lucon dot org]

------- Comment #22 from hjl at lucon dot org  2006-05-30 16:08 -------
Tonto in SPEC CPU 2006 should work now with gcc 4.1 and 4.2.


-- 

hjl at lucon dot org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
  BugsThisDependsOn|                            |27662
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED
            Summary|[meta-bug] Gfortran can't   |[meta-bug] Gfortran can't
                   |compile tonto               |compile tonto correctly
Bug 26106 depends on bug 27662, which changed state.

Bug 27662 Summary: [4.1 only]: Transpose doesn't work on function return
http://gcc.gnu.org/bugzilla/show_bug.cgi?id=27662

           What    |Old Value                   |New Value
----------------------------------------------------------------------------
             Status|UNCONFIRMED                 |NEW
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED
             Status|RESOLVED                    |REOPENED
         Resolution|FIXED                       |
             Status|REOPENED                    |ASSIGNED

http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto correctly

[hjl at lucon dot org]

------- Comment #23 from hjl at lucon dot org  2006-07-30 23:27 -------
Tonto failed to build again.


-- 

hjl at lucon dot org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
  BugsThisDependsOn|                            |28548
             Status|RESOLVED                    |REOPENED
         Resolution|FIXED                       |


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto correctly

[paul dot richard dot thomas at cea dot fr]

------- Comment #24 from paul dot richard dot thomas at cea dot fr  2006-08-10 12:11 -------
(In reply to comment #23)
> Tonto failed to build again.

HJ

Can we close this again?  Steve's patch fixed the problem, as far as I know.

Regards

Paul Thomas


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106

[Bug fortran/26106] [meta-bug] Gfortran can't compile tonto correctly

[hjl at lucon dot org]

------- Comment #25 from hjl at lucon dot org  2006-08-10 16:40 -------
It is fixed in 4.2 now.


-- 

hjl at lucon dot org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|REOPENED                    |RESOLVED
         Resolution|                            |FIXED


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26106