[Bug fortran/32391] New: Default optimization (level 1) bug of loop optimization (maybe)

[Bug fortran/32391] New: Default optimization (level 1) bug of loop optimization (maybe)

[sunjoong at gmail dot com]

This bug occurs on gfortran 4.1 and 4.2 .
I think it is not a gfortran specific bug; I checked g77 and g95 on gcc 3.4.6..


I had compiled a legacy fortran77 code and foud a bug;

    $ gfortran -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
    Aligned length=  89, RMSD=  6.41, TM-score= 0.24257, ID=0.042

    $ gfortran -O0 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
    Aligned length=  91, RMSD=  6.35, TM-score=0.24762 , ID=0.024

    $ pgf77 -O1 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
    Aligned length=  91, RMSD=  6.35, TM-score=0.24762, ID= 0.024

$ pgf77 -O0 -o TMalign TMalign.f
$ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
Aligned length=  91, RMSD=  6.35, TM-score=0.24762, ID=0.024



That optimization error is on a bellow subroutine;

********************************************************************
*     Dynamic programming for alignment.
*     Input: score(i,j), and gap_open
*     Output: invmap(j)
********************************************************************
      SUBROUTINE DP(NSEQ1,NSEQ2)
      PARAMETER(nmax=5000)
      LOGICAL*1 DIR
      common/dpc/score(nmax,nmax),gap_open,invmap(nmax)
      dimension DIR(0:nmax,0:nmax),VAL(0:nmax,0:nmax)
      REAL H,V

***   initialize the matrix:
      val(0,0)=0
      do i=1,nseq1
        dir(i,0)=.false.
        val(i,0)=0
      enddo
      do j=1,nseq2
        dir(0,j)=.false.
        val(0,j)=0
        invmap(j)=-1
      enddo

***   decide matrix and path:
      DO j=1,NSEQ2
        DO i=1,NSEQ1
          D=VAL(i-1,j-1)+SCORE(i,j)
          H=VAL(i-1,j)
          if(DIR(i-1,j))H=H+GAP_OPEN
          V=VAL(i,j-1)
          if(DIR(i,j-1))V=V+GAP_OPEN

          IF(( D.GE.H).AND.(D.GE.V)) THEN
            DIR(I,J)=.true.
            VAL(i,j)=D
          ELSE
            DIR(I,J)=.false.
            if(V.GE.H)then
              val(i,j)=v
            else
              val(i,j)=h
            end if
          ENDIF
        ENDDO
      ENDDO

***   extract the alignment:
      i=NSEQ1
      j=NSEQ2
      DO WHILE((i.GT.0).AND.(j.GT.0))
        IF(DIR(i,j))THEN
          invmap(j)=i
          i=i-1
          j=j-1
        ELSE
          H=VAL(i-1,j)
          if(DIR(i-1,j))H=H+GAP_OPEN
          V=VAL(i,j-1)
          if(DIR(i,j-1))V=V+GAP_OPEN
          IF( V.GE.H) THEN
            j=j-1
          ELSE
            i=i-1
          ENDIF
        ENDIF
      ENDDO

c^^^^^^^^^^^^^^^Dynamical programming done ^^^^^^^^^^^^^^^^^^^
      return
      END 


Files;

http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f
http://zhang.bioinformatics.ku.edu/TM-align/benchmark/1aquA.pdb
http://zhang.bioinformatics.ku.edu/TM-align/benchmark/1avaC.pdb


-- 
           Summary: Default optimization (level 1) bug of loop optimization
                    (maybe)
           Product: gcc
           Version: 4.2.0
            Status: UNCONFIRMED
          Severity: normal
          Priority: P3
         Component: fortran
        AssignedTo: unassigned at gcc dot gnu dot org
        ReportedBy: sunjoong at gmail dot com
 GCC build triplet: i686-pc-linux-gnu
  GCC host triplet: i686-pc-linux-gnu
GCC target triplet: i686-pc-linux-gnu


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Default optimization (level 1) bug of loop optimization (maybe)

[sunjoong at gmail dot com]

------- Comment #2 from sunjoong at gmail dot com  2007-06-18 14:19 -------
Created an attachment (id=13728)
 --> (http://gcc.gnu.org/bugzilla/attachment.cgi?id=13728&action=view)
A input data file of TMalign


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Default optimization (level 1) bug of loop optimization (maybe)

[sunjoong at gmail dot com]

------- Comment #1 from sunjoong at gmail dot com  2007-06-18 14:18 -------
Created an attachment (id=13727)
 --> (http://gcc.gnu.org/bugzilla/attachment.cgi?id=13727&action=view)
A legacy fortran77 program


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Default optimization (level 1) bug of loop optimization (maybe)

[sunjoong at gmail dot com]

------- Comment #3 from sunjoong at gmail dot com  2007-06-18 14:20 -------
Created an attachment (id=13729)
 --> (http://gcc.gnu.org/bugzilla/attachment.cgi?id=13729&action=view)
A input data file of TMalign


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Generate wrong optimization code from fortran 77

[sunjoong at gmail dot com]

------- Comment #4 from sunjoong at gmail dot com  2007-06-18 15:08 -------
Thank you, Tobias

I had missunderstood the default optimization level for gfortran
but the issue exists, I think.

I had traced side effects of optimization levels for the legacy program;
    -O0 level and -O1 level were different
    but from -O1 to -O3 gave same (wrong) results on gfortran, g77 and g95.
    I tested it with pgi fortran and got same (right) results.

I checked gfortran 4.0.4, 4.1.2 and 4.2.0.
I did not check gfortran 4.3.

2007/6/18, Tobias Burnus <burnus@net-b.de>:
> Sunjoong Lee wrote:
> > I had compiled a legacy fortran77 code and foud a bug;
> >    $ gfortran -o TMalign TMalign.f
> >    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
> >    Aligned length=  89, RMSD=  6.41, TM-score= 0.24257, ID=0.042
> >    $ gfortran -O0 -o TMalign TMalign.f
> >    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
> >    Aligned length=  91, RMSD=  6.35, TM-score=0.24762 , ID=0.024
> I find this difference very odd as "-O0" is the default optimization for
> gfortran. Other than that I get always the same result  ("91") with all
> -O levels I tried with gfortran 4.3, 4.2.0, 4.1.3 and ifort.
> 
> Which version of the compiler are you using on which platform. (Use
> "gfortran -v" to shows this information.)
> Can you also show what "alias gfortran" (or "type gfortran") shows? Just
> to make sure there is no alias which adds options.
> 
> Tobias
> 


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Generate wrong optimization code on fortran 77

[dominiq at lps dot ens dot fr]

------- Comment #5 from dominiq at lps dot ens dot fr  2007-06-18 15:38 -------
I did not make as many tests as Tobias, but it "works" for me on PPC with g77,
xlf, g95, and gfortran.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Generate wrong optimization code on fortran 77

[sunjoong at gmail dot com]

------- Comment #6 from sunjoong at gmail dot com  2007-06-18 16:07 -------
Thanks again, Tobias

$ uname -a
Linux newton 2.6.12-gentoo-r10 #1 Sun Sep 4 13:29:37 KST 2005 i686 Intel(R)
Pentium(R) 4 CPU 2.40GHz GenuineIntel GNU/Linux

$ gfortran -v
Using built-in specs.
Target: i686-pc-linux-gnu
Configured with: /var/tmp/portage/sys-devel/gcc-4.1.2/work/gcc-4.1.2/configure
--prefix=/usr --bindir=/usr/i686-pc-linux-gnu/gcc-bin/4.1.2
--includedir=/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/include
--datadir=/usr/share/gcc-data/i686-pc-linux-gnu/4.1.2
--mandir=/usr/share/gcc-data/i686-pc-linux-gnu/4.1.2/man
--infodir=/usr/share/gcc-data/i686-pc-linux-gnu/4.1.2/info
--with-gxx-include-dir=/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/include/g++-v4
--host=i686-pc-linux-gnu --build=i686-pc-linux-gnu --disable-altivec
--enable-nls --without-included-gettext --with-system-zlib --disable-checking
--disable-werror --enable-secureplt --disable-libunwind-exceptions
--disable-multilib --enable-libmudflap --disable-libssp --disable-libgcj
--enable-languages=c,c++,fortran --enable-shared --enable-threads=posix
--enable-__cxa_atexit --enable-clocale=gnu
Thread model: posix
gcc version 4.1.2 (Gentoo 4.1.2)


I had tested it with this step;

    $ gfortran -O0 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
    $ gfortran -O1 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali

    $ wget -O - http://ftp.g95.org/g95-x86-linux.tgz | tar xvfz -
    $ export PATH="$PATH:./g95-install/bin"
    $ g95 -O0 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
    $ g95 -O1 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali

    $ emerge =sys-devel/gcc-4.2.0                                     # install
gcc-4.2.0 and gfortran
    $ gcc-config i686-pc-linux-gnu-4.2.0
    $ source /etc/profile
    $ epm -e =sys-devel/gcc-4.1.2                                      # remove
gcc-4.1.2

    $ gfortran -O0 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
    $ gfortran -O1 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali

    $ emerge =sys-devel/gcc-4.0.4                                     # install
gcc-4.0.4 and gfortran
    $ gcc-config i686-pc-linux-gnu-4.0.4
    $ source /etc/profile
    $ epm -e =sys-devel/gcc-4.2.0                                      # remove
gcc-4.2.0

    $ gfortran -O0 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
    $ gfortran -O1 -o TMalign TMalign.f
    $ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali


After then, I loged in another machine;

$ uname -a
Linux gene.kias.re.kr 2.6.3-gene #3 SMP Wed Jan 19 00:10:01 KST 2005 i686
unknown unknown GNU/Linux

$ g77 -v
Reading specs from /usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.3.2/specs
Configured with: ../configure --prefix=/usr --libdir=/usr/lib
--with-slibdir=/lib --mandir=/usr/share/man --infodir=/usr/share/info
--enable-shared --enable-threads=posix --disable-checking --enable-long-long
--enable-__cxa_atexit --enable-clocale=gnu
--enable-languages=c,c++,ada,f77,objc,java,pascal
--host=i586-mandrake-linux-gnu --with-system-zlib
Thread model: posix
gcc version 3.3.2 (Mandrake Linux 10.0 3.3.2-6mdk)

$ g77 -O0 -o TMalign TMalign.f
$ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
$ g77 -O1 -o TMalign TMalign.f
$ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali

$ pgf77 -O0 -o TMalign TMalign.f
$ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali
$ pgf77 -O1 -o TMalign TMalign.f
$ ./TMalign 1aquA.pdb 1avaC.pdb | grep ^Ali


Which do you think the reson for this difference be for fortran compiler or c
compiler?

2007/6/19, Tobias Burnus <burnus@net-b.de>:
> As said: It works here with 4.1.3 20070521, 4.2.1 20070604 and 20070618,
> 4.3.0 20070618. It also work with my g95, Intel Fortran and sunf95
> compilers. In all cases I get:
> 
> Aligned length=  91, RMSD=  6.35, TM-score=0.24762, ID=0.024
> 
> I'm on x86_64-unknown-linux-gnu (openSUSE Factory) and it works both in
> 32 and 64 bit mode with no option, -O0, -O1, -O2, -O3, -O3 -ffast-math.
> 
> 
> What is your platform (CPU type and operating system) and what is your
> exact version of gfortran? (Both information is shown by "gfortran -v".)
> (You are really only using "-O1" and not any other flags, are you?)
> 
> Tobias
> 


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[burnus at gcc dot gnu dot org]

------- Comment #7 from burnus at gcc dot gnu dot org  2007-06-18 16:38 -------
> $ gfortran -v
> Target: i686-pc-linux-gnu
> gcc version 4.1.2 (Gentoo 4.1.2)

I can reproduce this on my Pentium M (openSUSE 10.2) with
  Target: i586-suse-linux
  gcc version 4.1.2 20061115 (prerelease) (SUSE Linux)
and with FX's
  Target: i386-pc-linux-gnu
  gcc version 4.3.0 20070618 (experimental)

Interestingly, it works on x86_64-unknown-linux-gnu even with -m32.
(I somehow fail to run FX's i386 compiler on x86-64.)

I think this could be a middle-end or target problem as it is that target
dependent. On the other hand, gfortran (and g95) could simply produce a wrong
generic code.


-- 

burnus at gcc dot gnu dot org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |burnus at gcc dot gnu dot
                   |                            |org
             Status|UNCONFIRMED                 |NEW
     Ever Confirmed|0                           |1
      Known to fail|                            |4.1.2 4.3.0
   Last reconfirmed|0000-00-00 00:00:00         |2007-06-18 16:38:39
               date|                            |
            Summary|Generate wrong optimization |Wrong code with optimization
                   |code on fortran 77          |on i686-pc-linux-gnu


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[sunjoong at gmail dot com]

------- Comment #8 from sunjoong at gmail dot com  2007-06-18 17:26 -------
I checked which part of TMalign.f make optimizaton wrong;
In DP subroutine,

      DO j=1,NSEQ2
        DO i=1,NSEQ1
          D=VAL(i-1,j-1)+SCORE(i,j)
          H=VAL(i-1,j)
          if(DIR(i-1,j))H=H+GAP_OPEN
          V=VAL(i,j-1)
          if(DIR(i,j-1))V=V+GAP_OPEN

          IF((D.GE.H).AND.(D.GE.V)) THEN
            DIR(I,J)=.true.
            VAL(i,j)=D
          ELSE
            DIR(I,J)=.false.
            if(V.GE.H)then
              val(i,j)=v
            else
              val(i,j)=h
            end if
          ENDIF
        ENDDO
      ENDDO


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[sunjoong at gmail dot com]

------- Comment #9 from sunjoong at gmail dot com  2007-06-18 18:31 -------
I cut the bellow and made a new subroutine,
then another part did not change on '-O0' and '-O1';

          D=VAL(i-1,j-1)+SCORE(i,j)
          H=VAL(i-1,j)
          if(DIR(i-1,j))H=H+GAP_OPEN
          V=VAL(i,j-1)
          if(DIR(i,j-1))V=V+GAP_OPEN

          IF((D.GE.H).AND.(D.GE.V)) THEN
            DIR(I,J)=.true.
            VAL(i,j)=D
          ELSE
            DIR(I,J)=.false.
            if(V.GE.H)then
              val(i,j)=v
            else
              val(i,j)=h
            end if
          ENDIF


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[kargl at gcc dot gnu dot org]

------- Comment #10 from kargl at gcc dot gnu dot org  2007-06-18 18:36 -------
There are literal hundreds of warning given by ftnchek, and there
appears to be an array bounds problem.

troutmask:sgk[231] gfc4x -o z -O -fbounds-check TMalign.f
troutmask:sgk[232] ./z 1aquA.pdb 1avaC.pdb | grep RMSD
At line 2122 of file TMalign.f
Fortran runtime error: Array reference out of bounds for array 'w', upper bound
+of dimension 1 exceeded


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[sunjoong at gmail dot com]

------- Comment #11 from sunjoong at gmail dot com  2007-06-18 18:47 -------
Yes, I agree that program is not beautiful
and I know the the array 'w' of 'u3b' subroutine problem;
I think the author of u3b use w(1) as pointer.

However,
the wrong generation of optimized code occurs in 'DP' subroutine.
The array of DP have fixed boundary.

(In reply to comment #10)
> There are literal hundreds of warning given by ftnchek, and there
> appears to be an array bounds problem.
> 
> troutmask:sgk[231] gfc4x -o z -O -fbounds-check TMalign.f
> troutmask:sgk[232] ./z 1aquA.pdb 1avaC.pdb | grep RMSD
> At line 2122 of file TMalign.f
> Fortran runtime error: Array reference out of bounds for array 'w', upper bound
> +of dimension 1 exceeded
> 


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[kargl at gcc dot gnu dot org]

------- Comment #12 from kargl at gcc dot gnu dot org  2007-06-18 19:16 -------
(In reply to comment #11)
> Yes, I agree that program is not beautiful
> and I know the the array 'w' of 'u3b' subroutine problem;
> I think the author of u3b use w(1) as pointer.

Change the 1 to *.

> However,
> the wrong generation of optimized code occurs in 'DP' subroutine.
> The array of DP have fixed boundary.

Do you get wrong results if you add the -ffloat-store option?
Can you also try the -fdefault-real-8 option?


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[sunjoong at gmail dot com]

------- Comment #13 from sunjoong at gmail dot com  2007-06-18 20:24 -------
The '-ffloat-store' option works! Thank you.

However that gave me some quenstions;

    Is that feature or bug?

    There is many floating point operations of course.
    Why the only one specific resion make problem?

    That is not set when optimize.
    So, what's the disadvantage and
    why the 'fortran' with many floating point operation
    dosn't take it when optimize?

    Why x86 need that option but x86_64 or PPC do not need?

(In reply to comment #12)
> Do you get wrong results if you add the -ffloat-store option?
> Can you also try the -fdefault-real-8 option?


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[kargl at gcc dot gnu dot org]

------- Comment #14 from kargl at gcc dot gnu dot org  2007-06-18 20:47 -------
(In reply to comment #13)
> The '-ffloat-store' option works! Thank you.
> 
> However that gave me some quenstions;
> 
>     Is that feature or bug?

It is a 'feature' of the i386 class of cpu.  See PR 323 for 
details.

>     There is many floating point operations of course.
>     Why the only one specific resion make problem?

The floating point operations are done with 80-bit 
precision and the intermediate results that are left
in a register have the extra precision.  Double precision
has 53 bits of precision and single precision has 24
bits.  The mixed mode arithmetic that ftnchek warns
about can cause the type of problem you are seeing.
The -ffloat-store option forces the contents in a register
after a floating pointing operation to be written to main
memory and then re-read.  This removes the extra precision.


>     That is not set when optimize.
>     So, what's the disadvantage and
>     why the 'fortran' with many floating point operation
>     dosn't take it when optimize?

You'll need to review the code.  I'd suggest first eliminating
the warns produced by ftnchek.  If the problems disappear, then
be happy.  If the problems are still present, you'll need to 
review the floating point operations in the code.


>     Why x86 need that option but x86_64 or PPC do not need?

These cpus do not store intermediate results in 80-bit register.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[pinskia at gcc dot gnu dot org]

------- Comment #15 from pinskia at gcc dot gnu dot org  2007-06-19 08:11 -------
So this is just a dup of bug 323 so closing as such.

*** This bug has been marked as a duplicate of 323 ***


-- 

pinskia at gcc dot gnu dot org changed:

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


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[sunjoong at gmail dot com]

------- Comment #16 from sunjoong at gmail dot com  2007-06-20 23:34 -------
Thank all of you.
I could understand what make it different.

There is no 'volatile' statement in fortran77 syntax of gfortran.
Of course, volatile is not fortran77 standard, I think,
but a certian implimentation support volatile.
http://web.utk.edu/~prdaves/Computerhelp/Fortran_Reference/fortran_statements.htm

I made a bellow c function and checked it happends.
Yes, the problem is same
but in the c function, I can use 'volatile' keyword and be happy.
(I hope the next version of gfortran support volatile statement in fortran 77.)

C language version of decide subroutine (or decide_ function);
    #define NMAX 5000

    extern struct {
        float SCORE[NMAX][NMAX];
        float GAP_OPEN;
        int INVMAP[NMAX];
    } dpc_;

    void
    decide_(int *i, int *j,
        int iDIR[NMAX + 1][NMAX + 1], float VAL[NMAX + 1][NMAX + 1])
    {
        volatile float D;
        float H,V;

        D = VAL[*j - 1][*i - 1] + dpc_.SCORE[*j - 1][*i - 1];
        if(iDIR[*j][*i - 1] == 1) H = VAL[*j][*i - 1] + dpc_.GAP_OPEN;
        else                      H = VAL[*j][*i - 1];
        if(iDIR[*j - 1][*i] == 1) V = VAL[*j - 1][*i] + dpc_.GAP_OPEN;
        else                      V = VAL[*j - 1][*i];

        if((D >= H) && (D >= V))
        {
            iDIR[*j][*i] = 1;
            VAL[*j][*i] = D;
        } else {
            iDIR[*j][*i] = 0;
            if(V >= H) VAL[*j][*i] = V;
            else       VAL[*j][*i] = H;
        }
    }


DP subroutine use above decide subroutine;
      SUBROUTINE DP(NSEQ1,NSEQ2)
      PARAMETER(nmax=5000)
      common/dpc/score(nmax,nmax),gap_open,invmap(nmax)
      dimension iDIR(0:nmax,0:nmax),VAL(0:nmax,0:nmax)
      REAL H,V

C**   initialize the matrix:
      val(0,0)=0
      do i=1,nseq1
        idir(i,0)=0
        val(i,0)=0
      enddo
      do j=1,nseq2
        idir(0,j)=0
        val(0,j)=0
        invmap(j)=-1
      enddo

C**   decide matrix and path:
      DO j=1,NSEQ2
        DO i=1,NSEQ1
         call decide(i,j,iDIR,VAL)
        ENDDO

C**   extract the alignment:
      i=NSEQ1
      j=NSEQ2
      DO WHILE((i.GT.0).AND.(j.GT.0))
        IF(iDIR(i,j).eq.1)THEN
          invmap(j)=i
          i=i-1
          j=j-1
        ELSE
          H=VAL(i-1,j)
          if(iDIR(i-1,j).eq.1)H=H+GAP_OPEN
          V=VAL(i,j-1)
          if(iDIR(i,j-1).eq.1)V=V+GAP_OPEN
          IF(V.GE.H) THEN
            j=j-1
          ELSE
            i=i-1
          ENDIF
        ENDIF
      ENDDO

      return
      END


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[kargl at gcc dot gnu dot org]

------- Comment #17 from kargl at gcc dot gnu dot org  2007-06-21 02:24 -------
(In reply to comment #16)
> Thank all of you.
> I could understand what make it different.
> 
> There is no 'volatile' statement in fortran77 syntax of gfortran.
> Of course, volatile is not fortran77 standard, I think,
> but a certian implimentation support volatile.

You need to update the Fortran Standard that you use.  Fortran
77 hasn't been the standard since about 1990.  In fact, you're
3 standard been!  There was Fortran 90, which was replaced by
Fortran 95, which was replaced by Fortran 2003.  Fortran 2003 
has the VOLATILE attribute and VOLATILE statement.  Guess what??
No, go ahead and guess!  gfortran supports this feature.

You need to go read Goldberg's paper about floating point arithmetic.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[sunjoong at gmail dot com]

------- Comment #18 from sunjoong at gmail dot com  2007-06-21 03:27 -------
I appreciate kargl's comments; they were helpful.
I had known there is VOLATILE attribute in new Fortran standard
but I had worked with "LEGACY" fortran77 program!

I'll write C code if I shuld write one; that is more compatable for me.
However there are many legacy fortran 77 code in my field
and I don't want to rewrite it.

Small adjustment like '-ffloat-store'
when compiling by gfortran instead of pgf77
is acceptable
for I understood the behavior of register kargl told me.
(I had read Goldberg's briefly but that is not point.)

I had ONLY HOPEd VOLATILE statement in fortran 77 EXTENSION of gfortran.
I thought that would be convenient
on small modification of legacy fortran 77 program.

(In reply to comment #17)
> You need to update the Fortran Standard that you use.  Fortran
> 77 hasn't been the standard since about 1990.  In fact, you're
> 3 standard been!  There was Fortran 90, which was replaced by
> Fortran 95, which was replaced by Fortran 2003.  Fortran 2003 
> has the VOLATILE attribute and VOLATILE statement.  Guess what??
> No, go ahead and guess!  gfortran supports this feature.
> 
> You need to go read Goldberg's paper about floating point arithmetic.
> 


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[kargl at gcc dot gnu dot org]

------- Comment #19 from kargl at gcc dot gnu dot org  2007-06-21 04:08 -------
(In reply to comment #18)
> 
> I had ONLY HOPEd VOLATILE statement in fortran 77 EXTENSION of gfortran.
> I thought that would be convenient
> on small modification of legacy fortran 77 program.

You've completed missed the point!  gfortran is a Fortran 95
compiler with some Fortran 2003 extensions.  A valid Fortran
77 code is a valid Fortran 95 code.

You can add VOLATILE statements to your old legacy code and
gfortran will compile it.


-- 

kargl at gcc dot gnu dot org changed:

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http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[sunjoong at gmail dot com]

------- Comment #20 from sunjoong at gmail dot com  2007-06-21 04:35 -------
$ gfortran -O1 -o TMalign TMalign.f 
 In file TMalign.f:2005

      VOLATILE D                                                        
     1
Error: Unclassifiable statement at (1)

(In reply to comment #19)
> You can add VOLATILE statements to your old legacy code and
> gfortran will compile it.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[kargl at gcc dot gnu dot org]

------- Comment #21 from kargl at gcc dot gnu dot org  2007-06-21 04:54 -------
(In reply to comment #20)
> $ gfortran -O1 -o TMalign TMalign.f 
>  In file TMalign.f:2005
> 
>       VOLATILE D                                                        
>      1
> Error: Unclassifiable statement at (1)

Sigh.  Try it with gfortran 4.3.0.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391

[Bug fortran/32391] Wrong code with optimization on i686-pc-linux-gnu

[sunjoong at gmail dot com]

------- Comment #22 from sunjoong at gmail dot com  2007-06-21 09:14 -------
I checked VOLATILE statement passing in gfortran 4.3 .

Unfortunately I had failed to buid gfortran (and gcc) 4.3 in my i686,
I only checked that passing with ia64 binary on another ia64 machine. 
(There is no gfortran 4.3 binary on i686.)

However, I think and hope it would work after my success of building on i686.

(In reply to comment #21)
> (In reply to comment #20)
> > $ gfortran -O1 -o TMalign TMalign.f 
> >  In file TMalign.f:2005
> > 
> >       VOLATILE D                                                        
> >      1
> > Error: Unclassifiable statement at (1)
> 
> Sigh.  Try it with gfortran 4.3.0.


-- 


http://gcc.gnu.org/bugzilla/show_bug.cgi?id=32391