[SciPy-user] segmentation fault in scipy.test()

gfunch gyromagnetic@gmail....
Sun Sep 7 11:15:22 CDT 2008


On Sun, Sep 7, 2008 at 9:27 AM, David Cournapeau
<david@ar.media.kyoto-u.ac.jp> wrote:
> gfunch wrote:
>> Hi,
>> I have tried to build SciPy (svn) on an x86_64 system running Linux
>> CentOS5, but ran into a segmentation fault while running the tests.
>>
>> I first compiled and installed Lapack and ATLAS per some instructions
>> I found the web. I then built and installed numpy (which tested fine)
>> and then built scipy.
>>
>> What commands should I run, and output should I generate, to best
>> diagnose the problem, and perhaps seek your kind help?
>>
>
> Hi Gyro,
>
>    Sorry for the bug in scipy. Could you give us the output when you
> run the tests (e.g. which test failed and segfaulted ?). Something
> useful would be the build log (output when run python setup.py
> build/install; we need the output when build from scratch, e.g. after
> having removed the build directory).
>    If you are familiar with gdb, something useful may be a backtrace,
> but first, I would like to check whether it is not a problem related to
> ATLAS/Lapack,
>
> cheers,
>
> David
> _______________________________________________
> SciPy-user mailing list
> SciPy-user@scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>

Hi David,
Thanks for the very prompt reply.

Below is the output you requested.

-gyro

-----
Here is the output of the tests:

$ python
Python 2.5.2 (r252:60911, Sep  5 2008, 07:14:57)
[GCC 4.1.2 20070626 (Red Hat 4.1.2-14)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test()
Running unit tests for scipy
NumPy version 1.2.0.dev5741
NumPy is installed in /home/gf/local/lib/python2.5/site-packages/numpy
SciPy version 0.7.0.dev4692
SciPy is installed in /home/gf/local/lib/python2.5/site-packages/scipy
Python version 2.5.2 (r252:60911, Sep  5 2008, 07:14:57) [GCC 4.1.2
20070626 (Red Hat 4.1.2-14)]
nose version 0.10.3

... [snip: a bunch of test results] ...

 warnings.warn(str1, DeprecationWarning)
.........E...........................FF.............ATLAS version
3.8.2 built by gf on Fri Sep  5 11:20:02 MDT 2008:
   UNAME    : Linux  2.6.18-53.el5xen #1 SMP Mon Nov 12 02:46:57 EST
2007 x86_64 x86_64 x86_64 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_PIII -DATL_CPUMHZ=2493
-DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 0
   F77      : gfortran, version GNU Fortran (GCC) 4.1.2 20070626 (Red
Hat 4.1.2-14)
   F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -fPIC -m64
   SMC      : gcc, version gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)
   SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -fPIC -m64
   SKC      : gcc, version gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)
   SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -fPIC -m64
.............................................F.Segmentation fault

-----

Here is the top of the output from
$ python setup.py build

mkl_info:
  libraries mkl,vml,guide not found in /home/gf/local/lib/
  libraries mkl,vml,guide not found in /home/gf/local/lib64/
  libraries mkl,vml,guide not found in /home/gf/local/lib/atlas
  libraries mkl,vml,guide not found in /usr/local/lib
  NOT AVAILABLE

fftw3_info:
  libraries fftw3 not found in /home/gf/local/lib/
  libraries fftw3 not found in /home/gf/local/lib64/
  libraries fftw3 not found in /home/gf/local/lib/atlas
  libraries fftw3 not found in /usr/local/lib
  fftw3 not found
  NOT AVAILABLE

fftw2_info:
  libraries rfftw,fftw not found in /home/gf/local/lib/
  libraries rfftw,fftw not found in /home/gf/local/lib64/
  libraries rfftw,fftw not found in /home/gf/local/lib/atlas
  libraries rfftw,fftw not found in /usr/local/lib
  fftw2 not found
  NOT AVAILABLE

dfftw_info:
  libraries drfftw,dfftw not found in /home/gf/local/lib/
  libraries drfftw,dfftw not found in /home/gf/local/lib64/
  libraries drfftw,dfftw not found in /home/gf/local/lib/atlas
  libraries drfftw,dfftw not found in /usr/local/lib
  dfftw not found
  NOT AVAILABLE

djbfft_info:
  NOT AVAILABLE

blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /home/gf/local/lib/
  libraries mkl,vml,guide not found in /home/gf/local/lib64/
  libraries mkl,vml,guide not found in /home/gf/local/lib/atlas
  libraries mkl,vml,guide not found in /usr/local/lib
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLASATLAS
Setting PTATLASATLAS
Setting PTATLASATLAS
  FOUND:
    libraries  ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs  ['/home/gf/local/lib/atlas']
    language  c

customize GnuFCompiler
Found executable /usr/bin/g77
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler 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 -fwrapv -O3
-Wall -Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/home/gf/local/lib/atlas -lptf77blas
-lptcblas -latlas -o _configtest
ATLAS version 3.8.2 built by  on Fri Sep  5 11:20:02 MDT 2008:
   UNAME    : Linux  2.6.18-53.el5xen #1 SMP Mon Nov 12 02:46:57 EST
2007 x86_64 x86_64 x86_6
4 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_PIII -DATL_CPUMHZ2493
-DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GA
S_x8664
   F2CDEFS  : -DAdd_ -DF77_INTEGERint -DStringSunStyle
   CACHEEDGE: 0
   F77      : gfortran, version GNU Fortran (GCC) 4.1.2 20070626 (Red
Hat 4.1.2-14)
   F77FLAGS : -fomit-frame-pointer -mfpmath387 -O2 -falign-loops4 -fPIC -m64
   SMC      : gcc, version gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)
   SMCFLAGS : -fomit-frame-pointer -mfpmath387 -O2 -falign-loops4 -fPIC -m64
   SKC      : gcc, version gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)
   SKCFLAGS : -fomit-frame-pointer -mfpmath387 -O2 -falign-loops4 -fPIC -m64
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries  ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs  ['/home/gf/local/lib/atlas']
    language  c
    define_macros  [('ATLAS_INFO', '"\\"3.8.2\\""')]

ATLAS version 3.8.2
lapack_opt_info:
lapack_mkl_info:
  NOT AVAILABLE

atlas_threads_info:
Setting PTATLASATLAS
  libraries lapack_atlas not found in /home/gf/local/lib/atlas
numpy.distutils.system_info.atlas_threads_info
Setting PTATLASATLAS
Setting PTATLASATLAS
  FOUND:
    libraries  ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs  ['/home/gf/local/lib/atlas']
    language  f77
	gnu: no Fortran 90 compiler found
	customize GnuFCompiler
	gnu: no Fortran 90 compiler found
	gnu: no Fortran 90 compiler found
	customize GnuFCompiler 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 -fwrapv -O3
-Wall -Wstrict-prototypes -fPIC

	compile options: '-c'
	gcc: _configtest.c
	gcc -pthread _configtest.o -L/home/gf/local/lib/atlas -llapack
-lptf77blas -lptcblas -latlas -o _configtest
	ATLAS version 3.8.2 built by  on Fri Sep  5 11:20:02 MDT 2008:
	   UNAME    : Linux 2.6.18-53.el5xen #1 SMP Mon Nov 12 02:46:57 EST
2007 x86_64 x86_64 x86_6
	4 GNU/Linux
	   INSTFLG  : -1 0 -a 1
	   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_PIII -DATL_CPUMHZ2493
-DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GA
	S_x8664
	   F2CDEFS  : -DAdd_ -DF77_INTEGERint -DStringSunStyle
	   CACHEEDGE: 0
	   F77      : gfortran, version GNU Fortran (GCC) 4.1.2 20070626 (Red
Hat 4.1.2-14)
	   F77FLAGS : -fomit-frame-pointer -mfpmath387 -O2 -falign-loops4 -fPIC -m64
	   SMC      : gcc, version gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)
	   SMCFLAGS : -fomit-frame-pointer -mfpmath387 -O2 -falign-loops4 -fPIC -m64
	   SKC      : gcc, version gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)
	   SKCFLAGS : -fomit-frame-pointer -mfpmath387 -O2 -falign-loops4 -fPIC -m64
	success!
	removing: _configtest.c _configtest.o _configtest
	  FOUND:
	    libraries  ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
	    library_dirs  ['/home/gf/local/lib/atlas']
	    language  f77
	    define_macros  [('ATLAS_INFO', '"\\"3.8.2\\""')]

	ATLAS version 3.8.2
	ATLAS version 3.8.2
	umfpack_info:
	  libraries umfpack not found in /home/gf/local/lib/
	  libraries umfpack not found in /home/gf/local/lib64/
	  libraries umfpack not found in /home/gf/local/lib/atlas
	  libraries umfpack not found in /usr/local/lib
	  NOT AVAILABLE


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