[SciPy-user] [SVN] scipy.test segmentation fault

LB berthe.loic@gmail....
Thu May 8 07:27:10 CDT 2008


   Hi,

I recerived sigsegv when running scipy.test() with a recent SVN
version.

Here are some information on this :

------------------ Installation log ------------------------
svn co http://svn.scipy.org/svn/scipy/trunk scipy
       [ ... ]
Révision 4244 extraite.
cd scipy

$python setup.py build  --fcompiler=gnu95
Warning: No configuration returned, assuming unavailable.
mkl_info:
  libraries mkl,vml,guide not found in /home/loic/tmp/bluelagoon/lib/
  NOT AVAILABLE

fftw3_info:
  FOUND:
    libraries = ['fftw3']
    library_dirs = ['/home/loic/tmp/bluelagoon/lib/']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/home/loic/tmp/bluelagoon/include/']

djbfft_info:
  NOT AVAILABLE

blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /home/loic/tmp/bluelagoon/lib/
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/home/loic/tmp/bluelagoon/lib/']
    language = c

customize GnuFCompiler
Found executable /home/loic/tmp/bluelagoon/bin/gfortran
gnu: no Fortran 90 compiler found
Found executable /usr/bin/g77
gnu: no Fortran 90 compiler found
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgf90
customize AbsoftFCompiler
customize NAGFCompiler
customize VastFCompiler
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize CompaqFCompiler
customize IntelItaniumFCompiler
Could not locate executable efort
Could not locate executable efc
customize IntelEM64TFCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -
Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/home/loic/tmp/bluelagoon/lib/ -llapack -
lf77blas -lcblas -latlas -o _configtest
ATLAS version 3.8.0 built by loic on mardi 4 mars 2008, 08:35:34 (UTC
+0100):
   UNAME    : Linux bluelagoon 2.6.22-3-686 #1 SMP Sun Feb 10 20:20:49
UTC 2008 i686 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_UNKNOWNx86 -DATL_CPUMHZ=2992 -
DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 2097152
   F77      : gfortran, version GNU Fortran (GCC) 4.2.3
   F77FLAGS : -O -fPIC -m32
   SMC      : gcc, version gcc (GCC) 4.2.3
   SMCFLAGS : -O -fomit-frame-pointer -fPIC -m32
   SKC      : gcc, version gcc (GCC) 4.2.3
   SKCFLAGS : -O -fomit-frame-pointer -fPIC -m32
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/home/loic/tmp/bluelagoon/lib/']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.8.0\\""')]

ATLAS version 3.8.0
lapack_opt_info:
lapack_mkl_info:
  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas not found in /home/loic/tmp/bluelagoon/lib/
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/home/loic/tmp/bluelagoon/lib/']
    language = f77

customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize IntelFCompiler
customize LaheyFCompiler
customize PGroupFCompiler
customize AbsoftFCompiler
customize NAGFCompiler
customize VastFCompiler
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize CompaqFCompiler
customize IntelItaniumFCompiler
customize IntelEM64TFCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -
Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/home/loic/tmp/bluelagoon/lib/ -llapack -
llapack -lf77blas -lcblas -latlas -o _configtest
ATLAS version 3.8.0 built by loic on mardi 4 mars 2008, 08:35:34 (UTC
+0100):
   UNAME    : Linux bluelagoon 2.6.22-3-686 #1 SMP Sun Feb 10 20:20:49
UTC 2008 i686 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_UNKNOWNx86 -DATL_CPUMHZ=2992 -
DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 2097152
   F77      : gfortran, version GNU Fortran (GCC) 4.2.3
   F77FLAGS : -O -fPIC -m32
   SMC      : gcc, version gcc (GCC) 4.2.3
   SMCFLAGS : -O -fomit-frame-pointer -fPIC -m32
   SKC      : gcc, version gcc (GCC) 4.2.3
   SKCFLAGS : -O -fomit-frame-pointer -fPIC -m32
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['lapack', 'lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/home/loic/tmp/bluelagoon/lib/']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.8.0\\""')]

ATLAS version 3.8.0
ATLAS version 3.8.0
umfpack_info:
amd_info:
  FOUND:
    libraries = ['amd']
    library_dirs = ['/home/loic/tmp/bluelagoon/lib/']
    swig_opts = ['-I/home/loic/tmp/bluelagoon/include']
    define_macros = [('SCIPY_AMD_H', None)]
    include_dirs = ['/home/loic/tmp/bluelagoon/include']

  FOUND:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/home/loic/tmp/bluelagoon/lib/']
    swig_opts = ['-I/home/loic/tmp/bluelagoon/include', '-I/home/loic/
tmp/bluelagoon/include']
    define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
    include_dirs = ['/home/loic/tmp/bluelagoon/include']

running build
   [...]

Writing /home/loic/tmp/bluelagoon/lib/python2.5/site-packages/
scipy-0.7.0.dev4244-py2.5.egg-info

----------------- Tests -------------------------------------
% gdb
python2.5
GNU gdb 6.7.1-debian
Copyright (C) 2007 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/
gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show
copying"
and "show warranty" for details.
This GDB was configured as "i486-linux-gnu"...
Using host libthread_db library "/lib/i686/cmov/libthread_db.so.1".
(gdb) run
Starting program: /home/loic/tmp/bluelagoon/bin/python2.5
[Thread debugging using libthread_db enabled]
Python 2.5.1 (r251:54863, Mar  4 2008, 18:22:16)
[GCC 4.2.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
[New Thread 0xb7e078c0 (LWP 17809)]
>>> import scipy
>>> scipy.test()
 [...]
...................................................SSSSSSSSSSS.....
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0xb7e078c0 (LWP 17809)]
0xb7102aac in next_char (fmt=0x8d0b068, literal=0) at ../.././
libgfortran/io/format.c:93
93	../.././libgfortran/io/format.c: No such file or directory.
	in ../.././libgfortran/io/format.c
(gdb) bt
#0  0xb7102aac in next_char (fmt=0x8d0b068, literal=0) at ../.././
libgfortran/io/format.c:93
#1  0xb7102b20 in format_lex (fmt=0x8d0b068) at ../.././libgfortran/io/
format.c:183
#2  0xb710384b in *_gfortrani_parse_format (dtp=0xbfcf3460) at ../.././
libgfortran/io/format.c:987
#3  0xb710d0e8 in data_transfer_init (dtp=0xbfcf3460, read_flag=0)
at ../.././libgfortran/io/transfer.c:1790
#4  0xb52790e5 in ivout_ () from /home/loic/tmp/bluelagoon/lib/
python2.5/site-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
#5  0x00000000 in ?? ()



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