octave-3.0.0 failed make check on pcg.m

[jli127]

octave-3.0.0
[/tmp/octave-3.0.0] uname -a
Linux lab6-10 2.6.18-gentoo-r7 #1 PREEMPT Tue Sep 11 15:10:26 EDT 2007 i686 Intel(R) Pentium(R) 4 CPU 2.66GHz GenuineIntel GNU/Linux

[/tmp/octave-3.0.0] gfortran -v
Using built-in specs.
Target: i686-pc-linux-gnu
Configured with: /tmp/portage/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 --disable-libmudflap --disable-libssp --enable-java-awt=gtk --enable-objc-gc --enable-languages=c,c++,java,objc,obj-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)


[/tmp/octave-3.0.0] make check
make -f octMakefile check
make[1]: Entering directory `/tmp/octave-3.0.0'
make -C test check
make[2]: Entering directory `/tmp/octave-3.0.0/test'
../run-octave --norc --silent --no-history ./fntests.m .

Integrated test scripts:

  src/DLD-FUNCTIONS/bsxfun.cc ............................ PASS   55/55
  src/DLD-FUNCTIONS/cellfun.cc ........................... PASS   31/31
  src/DLD-FUNCTIONS/conv2.cc ............................. PASS    1/1
  src/DLD-FUNCTIONS/dispatch.cc .......................... PASS   13/13
  src/DLD-FUNCTIONS/fft.cc ............................... PASS    9/9
  src/DLD-FUNCTIONS/fsolve.cc ............................ PASS    4/4
  src/DLD-FUNCTIONS/luinc.cc .............................
  src/DLD-FUNCTIONS/matrix_type.cc ....................... PASS   51/51
  src/DLD-FUNCTIONS/rand.cc .............................. PASS   57/57
  src/DLD-FUNCTIONS/regexp.cc ............................ PASS   81/81
  src/DLD-FUNCTIONS/spkron.cc ............................ PASS    2/2
  src/DLD-FUNCTIONS/spqr.cc .............................. PASS    2/2
  src/DLD-FUNCTIONS/tsearch.cc ........................... PASS    6/6
  src/data.cc ............................................ PASS   20/20
  src/ov-fcn-handle.cc ................................... PASS    3/3
  src/ov-struct.cc ....................................... PASS   15/15
  src/pt-idx.cc .......................................... PASS    5/5
  src/strfns.cc .......................................... PASS   22/22
  src/syscalls.cc ........................................ PASS    1/1
  liboctave/CMatrix.cc ................................... PASS    6/6
  liboctave/dMatrix.cc ................................... PASS    6/6
  scripts/audio/wavwrite.m ............................... PASS    3/3
  scripts/elfun/acosd.m .................................. PASS    3/3
  scripts/elfun/acotd.m .................................. PASS    3/3
  scripts/elfun/acscd.m .................................. PASS    3/3
  scripts/elfun/asecd.m .................................. PASS    3/3
  scripts/elfun/asind.m .................................. PASS    3/3
  scripts/elfun/atand.m .................................. PASS    3/3
  scripts/elfun/cosd.m ................................... PASS    5/5
  scripts/elfun/cotd.m ................................... PASS    5/5
  scripts/elfun/cscd.m ................................... PASS    5/5
  scripts/elfun/secd.m ................................... PASS    5/5
  scripts/elfun/sind.m ................................... PASS    5/5
  scripts/elfun/tand.m ................................... PASS    5/5
  scripts/general/__isequal__.m .......................... PASS   26/26
  scripts/general/accumarray.m ........................... PASS   11/11
  scripts/general/arrayfun.m ............................. PASS    1/1
  scripts/general/bitcmp.m ............................... PASS   15/15
  scripts/general/blkdiag.m .............................. PASS    8/8
  scripts/general/cell2mat.m ............................. PASS    2/2
  scripts/general/cplxpair.m ............................. PASS   13/13
  scripts/general/cumtrapz.m ............................. PASS    6/6
  scripts/general/deal.m ................................. PASS    2/2
  scripts/general/interp1.m .............................. PASS  144/144
  scripts/general/interp2.m .............................. PASS    6/6
  scripts/general/interp3.m .............................. PASS    1/1
  scripts/general/interpft.m ............................. PASS    5/5
  scripts/general/issymmetric.m .......................... PASS   12/12
  scripts/general/lookup.m ............................... PASS   13/13
  scripts/general/mod.m .................................. PASS   18/18
  scripts/general/nthroot.m .............................. PASS    3/3
  scripts/general/polyarea.m ............................. PASS    4/4
  scripts/general/repmat.m ............................... PASS   16/16
  scripts/general/structfun.m ............................ PASS    1/1
  scripts/general/sub2ind.m .............................. PASS   24/24
  scripts/general/trapz.m ................................ PASS    6/6
  scripts/geometry/convhull.m ............................ PASS    0/1    FAIL 1
  scripts/geometry/delaunay.m ............................ PASS    0/1    FAIL 1
  scripts/geometry/delaunay3.m ........................... PASS    0/1    FAIL 1
  scripts/geometry/dsearch.m ............................. PASS    2/2
  scripts/geometry/dsearchn.m ............................ PASS    6/6
  scripts/geometry/griddata.m ............................ PASS    0/1    FAIL 1
  scripts/geometry/griddatan.m ........................... PASS    0/2    FAIL 2
  scripts/geometry/tsearchn.m ............................ PASS    5/5
  scripts/image/imshow.m ................................. PASS    3/3
  scripts/linear-algebra/condest.m ....................... PASS    4/4
  scripts/linear-algebra/onenormest.m .................... PASS    4/4
  scripts/miscellaneous/bincoeff.m ....................... PASS    3/3
  scripts/miscellaneous/compare_versions.m ............... PASS   30/30
  scripts/miscellaneous/fullfile.m ....................... PASS   13/13
  scripts/miscellaneous/getfield.m ....................... PASS    2/2
  scripts/miscellaneous/inputname.m ...................... PASS    2/2
  scripts/miscellaneous/setfield.m ....................... PASS    2/2
  scripts/miscellaneous/substruct.m ...................... PASS    6/6
  scripts/plot/hist.m .................................... PASS    6/6
  scripts/plot/orient.m .................................. PASS    7/7
  scripts/polynomial/pchip.m ............................. PASS    7/7
  scripts/polynomial/residue.m ........................... PASS    4/4
  scripts/polynomial/spline.m ............................ PASS   16/16
  scripts/set/intersect.m ................................ PASS    1/1
  scripts/set/ismember.m ................................. PASS   25/25
  scripts/set/setdiff.m .................................. PASS    7/7
  scripts/set/setxor.m ................................... PASS    1/1
  scripts/set/unique.m ................................... PASS    9/9
  scripts/signal/detrend.m ............................... PASS    3/3
  scripts/signal/freqz.m ................................. PASS    3/3
  scripts/sparse/nonzeros.m .............................. PASS    2/2
  scripts/sparse/pcg.m ...................................panic: Illegal instruction -- stopping myself...
make[2]: *** [check] Illegal instruction
make[2]: Leaving directory `/tmp/octave-3.0.0/test'
make[1]: *** [check] Error 2
make[1]: Leaving directory `/tmp/octave-3.0.0'
make: *** [check] Error 2

How to fix it? Thanks

JL

[John W. Eaton]

On 14-Jan-2008, jli127 wrote:

|
| octave-3.0.0
| [/tmp/octave-3.0.0] uname -a
| Linux lab6-10 2.6.18-gentoo-r7 #1 PREEMPT Tue Sep 11 15:10:26 EDT 2007 i686
| Intel(R) Pentium(R) 4 CPU 2.66GHz GenuineIntel GNU/Linux
|
| [/tmp/octave-3.0.0] gfortran -v
| Using built-in specs.
| Target: i686-pc-linux-gnu
| Configured with:
| /tmp/portage/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 --disable-libmudflap
| --disable-libssp --enable-java-awt=gtk --enable-objc-gc
| --enable-languages=c,c++,java,objc,obj-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)
|
|
| [/tmp/octave-3.0.0] make check
| make -f octMakefile check
| make[1]: Entering directory `/tmp/octave-3.0.0'
| make -C test check
| make[2]: Entering directory `/tmp/octave-3.0.0/test'
| ../run-octave --norc --silent --no-history ./fntests.m .
|
| Integrated test scripts:
|
|   src/DLD-FUNCTIONS/bsxfun.cc ............................ PASS   55/55
|   src/DLD-FUNCTIONS/cellfun.cc ........................... PASS   31/31
|   src/DLD-FUNCTIONS/conv2.cc ............................. PASS    1/1
|   src/DLD-FUNCTIONS/dispatch.cc .......................... PASS   13/13
|   src/DLD-FUNCTIONS/fft.cc ............................... PASS    9/9
|   src/DLD-FUNCTIONS/fsolve.cc ............................ PASS    4/4
|   src/DLD-FUNCTIONS/luinc.cc .............................
|   src/DLD-FUNCTIONS/matrix_type.cc ....................... PASS   51/51
|   src/DLD-FUNCTIONS/rand.cc .............................. PASS   57/57
|   src/DLD-FUNCTIONS/regexp.cc ............................ PASS   81/81
|   src/DLD-FUNCTIONS/spkron.cc ............................ PASS    2/2
|   src/DLD-FUNCTIONS/spqr.cc .............................. PASS    2/2
|   src/DLD-FUNCTIONS/tsearch.cc ........................... PASS    6/6
|   src/data.cc ............................................ PASS   20/20
|   src/ov-fcn-handle.cc ................................... PASS    3/3
|   src/ov-struct.cc ....................................... PASS   15/15
|   src/pt-idx.cc .......................................... PASS    5/5
|   src/strfns.cc .......................................... PASS   22/22
|   src/syscalls.cc ........................................ PASS    1/1
|   liboctave/CMatrix.cc ................................... PASS    6/6
|   liboctave/dMatrix.cc ................................... PASS    6/6
|   scripts/audio/wavwrite.m ............................... PASS    3/3
|   scripts/elfun/acosd.m .................................. PASS    3/3
|   scripts/elfun/acotd.m .................................. PASS    3/3
|   scripts/elfun/acscd.m .................................. PASS    3/3
|   scripts/elfun/asecd.m .................................. PASS    3/3
|   scripts/elfun/asind.m .................................. PASS    3/3
|   scripts/elfun/atand.m .................................. PASS    3/3
|   scripts/elfun/cosd.m ................................... PASS    5/5
|   scripts/elfun/cotd.m ................................... PASS    5/5
|   scripts/elfun/cscd.m ................................... PASS    5/5
|   scripts/elfun/secd.m ................................... PASS    5/5
|   scripts/elfun/sind.m ................................... PASS    5/5
|   scripts/elfun/tand.m ................................... PASS    5/5
|   scripts/general/__isequal__.m .......................... PASS   26/26
|   scripts/general/accumarray.m ........................... PASS   11/11
|   scripts/general/arrayfun.m ............................. PASS    1/1
|   scripts/general/bitcmp.m ............................... PASS   15/15
|   scripts/general/blkdiag.m .............................. PASS    8/8
|   scripts/general/cell2mat.m ............................. PASS    2/2
|   scripts/general/cplxpair.m ............................. PASS   13/13
|   scripts/general/cumtrapz.m ............................. PASS    6/6
|   scripts/general/deal.m ................................. PASS    2/2
|   scripts/general/interp1.m .............................. PASS  144/144
|   scripts/general/interp2.m .............................. PASS    6/6
|   scripts/general/interp3.m .............................. PASS    1/1
|   scripts/general/interpft.m ............................. PASS    5/5
|   scripts/general/issymmetric.m .......................... PASS   12/12
|   scripts/general/lookup.m ............................... PASS   13/13
|   scripts/general/mod.m .................................. PASS   18/18
|   scripts/general/nthroot.m .............................. PASS    3/3
|   scripts/general/polyarea.m ............................. PASS    4/4
|   scripts/general/repmat.m ............................... PASS   16/16
|   scripts/general/structfun.m ............................ PASS    1/1
|   scripts/general/sub2ind.m .............................. PASS   24/24
|   scripts/general/trapz.m ................................ PASS    6/6
|   scripts/geometry/convhull.m ............................ PASS    0/1  
| FAIL 1
|   scripts/geometry/delaunay.m ............................ PASS    0/1  
| FAIL 1
|   scripts/geometry/delaunay3.m ........................... PASS    0/1  
| FAIL 1
|   scripts/geometry/dsearch.m ............................. PASS    2/2
|   scripts/geometry/dsearchn.m ............................ PASS    6/6
|   scripts/geometry/griddata.m ............................ PASS    0/1  
| FAIL 1
|   scripts/geometry/griddatan.m ........................... PASS    0/2  
| FAIL 2
|   scripts/geometry/tsearchn.m ............................ PASS    5/5
|   scripts/image/imshow.m ................................. PASS    3/3
|   scripts/linear-algebra/condest.m ....................... PASS    4/4
|   scripts/linear-algebra/onenormest.m .................... PASS    4/4
|   scripts/miscellaneous/bincoeff.m ....................... PASS    3/3
|   scripts/miscellaneous/compare_versions.m ............... PASS   30/30
|   scripts/miscellaneous/fullfile.m ....................... PASS   13/13
|   scripts/miscellaneous/getfield.m ....................... PASS    2/2
|   scripts/miscellaneous/inputname.m ...................... PASS    2/2
|   scripts/miscellaneous/setfield.m ....................... PASS    2/2
|   scripts/miscellaneous/substruct.m ...................... PASS    6/6
|   scripts/plot/hist.m .................................... PASS    6/6
|   scripts/plot/orient.m .................................. PASS    7/7
|   scripts/polynomial/pchip.m ............................. PASS    7/7
|   scripts/polynomial/residue.m ........................... PASS    4/4
|   scripts/polynomial/spline.m ............................ PASS   16/16
|   scripts/set/intersect.m ................................ PASS    1/1
|   scripts/set/ismember.m ................................. PASS   25/25
|   scripts/set/setdiff.m .................................. PASS    7/7
|   scripts/set/setxor.m ................................... PASS    1/1
|   scripts/set/unique.m ................................... PASS    9/9
|   scripts/signal/detrend.m ............................... PASS    3/3
|   scripts/signal/freqz.m ................................. PASS    3/3
|   scripts/sparse/nonzeros.m .............................. PASS    2/2
|   scripts/sparse/pcg.m ...................................panic: Illegal
| instruction -- stopping myself...
| make[2]: *** [check] Illegal instruction
| make[2]: Leaving directory `/tmp/octave-3.0.0/test'
| make[1]: *** [check] Error 2
| make[1]: Leaving directory `/tmp/octave-3.0.0'
| make: *** [check] Error 2

It looks like you are missing some sparse tools.  What summary message
was printed when you ran configure?

| How to fix it? Thanks

Patch the tests in scripts/sparse/pcg.m so they don't execute when
necessary funcionality is missing, then submit the patch to us so we
can include it in future versions of Octave.

Oh, maybe you just meant how can you avoid the problem for yourself,
quickly?  In that case, install the sparse tools that Octave expects,
then reconfigure and rebuild.

jwe
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[dbateman3]

John W. Eaton wrote:
>
> It looks like you are missing some sparse tools.  What summary message
> was printed when you ran configure?

John,

pcg is an iterative solver, and doesn't rely on external libraries for
its functionality, except perhaps for a preconditioning step if the
preconditioner itself is sparse. So it depends how pcg was used. Also
the use of pcg is not limited to sparse matrices, and the matrices might
all very well be full.

I also would expect it to fail with an illegal instruction. I therefore
suspect that the issue here might be a buggy atlas/lapack build on the
platform in question like we've seen in the past, or the installation of
a version of atlas that is not adapted to the processor type.

>
> | How to fix it? Thanks
>
> Patch the tests in scripts/sparse/pcg.m so they don't execute when
> necessary funcionality is missing, then submit the patch to us so we
> can include it in future versions of Octave.

As the test are all with full matrices, this is not necessary.

> Oh, maybe you just meant how can you avoid the problem for yourself,
> quickly?  In that case, install the sparse tools that Octave expects,
> then reconfigure and rebuild.

Ditto for this as well.

D.


>
> jwe

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[John W. Eaton]

On 16-Jan-2008, David Bateman wrote:

| pcg is an iterative solver, and doesn't rely on external libraries for
| its functionality, except perhaps for a preconditioning step if the
| preconditioner itself is sparse.

OK, sorry for not checking more carefully.  Since pcg.m is in the
sparse directory, I assumed it required sparse stuff.  But I guess I
should have also realized that a crash shouldn't happen just because
of some missing functionality.

| I also would expect it to fail with an illegal instruction. I therefore
| suspect that the issue here might be a buggy atlas/lapack build on the
| platform in question like we've seen in the past, or the installation of
| a version of atlas that is not adapted to the processor type.

OK, then I think we would need some additional information to be able
to offer any help at all with debugging this problem.  I can't
reproduce it here.

jwe
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[jli127]

Thanks for your answers. Here is the output of configure by
> ./configure --disable-readline
cfg.gfortran
I suspect some of the fortran libraries on that machine have broken or the compilation linked the one with wrong version (the machine has 3.4.6, 4.1.1, 4.1.2). In the Makeconf, it says
FLIBS =  -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2 -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../.. -lz -lgfortranbegin -lgfortran -lm

Thanks, JL

[John W. Eaton]

On 16-Jan-2008, jli127 wrote:

|
| Thanks for your answers. Here is the output of configure by
| > ./configure --disable-readline
| http://www.nabble.com/file/p14884559/cfg.gfortran cfg.gfortran
| I suspect some of the fortran libraries on that machine have broken or the
| compilation linked the one with wrong version (the machine has 3.4.6, 4.1.1,
| 4.1.2). In the Makeconf, it says
| FLIBS =  -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2
| -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../../i686-pc-linux-gnu/lib
| -L/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../.. -lz -lgfortranbegin
| -lgfortran -lm

What version of g++/gcc are you using?  Is it also 4.1.2?

Although the configure macros that detect the Fortran compiler and set
FLIBS originated with Octave, they are now part of autoconf, so if
they are not working correctly, I think the problem should be reported
to the autoconf maintainers.

jwe
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[jli127]

jli127 wrote:

What version of g++/gcc are you using?  Is it also 4.1.2?

Yes, the g++/gcc is also 4.1.2.
The Makeconf was generated correctly, and compilation is succeed.
Here are configure and Makeconf
configureMakeconf

JL

[John W. Eaton]

On 16-Jan-2008, jli127 wrote:

|
|
|
| jli127 wrote:
| >
| > What version of g++/gcc are you using?  Is it also 4.1.2?
| >
| Yes, the g++/gcc is also 4.1.2.
| The Makeconf was generated correctly, and compilation is succeed.
| Here are configure and Makeconf
| http://www.nabble.com/file/p14889116/configure configure
| http://www.nabble.com/file/p14889116/Makeconf Makeconf

The configure script doesn't help all that much.  Makeconf is somewhat
useful, but doesn't have all the information that config.status has.

Like David, I suspect a problem with your BLAS/LAPACK libraries.

jwe

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[jli127]

John W. Eaton wrote:

On 16-Jan-2008, jli127 wrote:

The configure script doesn't help all that much.  Makeconf is somewhat
useful, but doesn't have all the information that config.status has.

Like David, I suspect a problem with your BLAS/LAPACK libraries.

jwe

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OK, I will try to replace those libraries. Thanks a lot.

JL