[SciPy-user] import of scipy.sparse.linalg is breaking

christopher taylor christopher.paul.taylor@gmail....
Thu Jan 15 09:23:49 CST 2009


Here is the output from ldd:

ldd _iterative.so
        libg2c.so.0 => /usr/lib64/libg2c.so.0 (0x00002b8b6f3b5000)
        libm.so.6 => /lib64/libm.so.6 (0x00002b8b6f5d6000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b8b6f859000)
        libc.so.6 => /lib64/libc.so.6 (0x00002b8b6fa68000)
        /lib64/ld-linux-x86-64.so.2 (0x0000003414800000)

I'm seeing this when I run the scipy build script (setup.py)

customize GnuFCompiler
Found executable /usr/bin/g77
gnu: no Fortran 90 compiler found

When scipy and numpy setup.py recognizes ATLAS it prints something
like this out:

ATLAS version 3.8.2

 INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_UNKNOWNx86 -DATL_CPUMHZ=3192
-DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 163840
   F77      : gfortran, version GNU Fortran (GCC) 4.1.2 20071124 (Red
Hat 4.1.2-42)
   F77FLAGS : -O -fPIC -m64
   SMC      : gcc, version gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
   SMCFLAGS : -O -fomit-frame-pointer -fPIC -m64
   SKC      : gcc, version gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
   SKCFLAGS : -O -fomit-frame-pointer -fPIC -m64

It also finds these libraries:

FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']

Thanks so much for your help!

ct

On Thu, Jan 15, 2009 at 9:34 AM, David Cournapeau <cournape@gmail.com> wrote:
> On Thu, Jan 15, 2009 at 11:02 PM, christopher taylor
> <christopher.paul.taylor@gmail.com> wrote:
>> Hello!
>>
>> I have built myself a copy of scipy 0.7.0 and have tried to import the
>> sparse.linalg module. I continue to get this error:
>>
>> Python 2.5.1 (r251:54863, Nov 25 2008, 17:51:08)
>> [GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> import scipy
>>>>> import scipy.sparse.linalg
>> Traceback (most recent call last):
>>  File "<stdin>", line 1, in <module>
>>  File "<path_to_python_site_packages>/scipy/sparse/linalg/__init__.py",
>> line 5, in <module>
>>    from isolve import *
>>  File "<path_to_python_site_packages>/scipy/sparse/linalg/isolve/__init__.py",
>> line 4, in <module>
>>    from iterative import *
>>  File "<path_to_python_site_packages>/scipy/sparse/linalg/isolve/iterative.py",
>> line 5, in <module>
>>    import _iterative
>> ImportError: <path_to_python_site_packages>/scipy/sparse/linalg/isolve/_iterative.so:
>> undefined symbol: slamch_
>>>>>
>>
>
> Which fortran compiler did you use to build blas/lapack, which one did
> you use for numpy and scipy ? Could you give us the output of ldd
> _iterative.so ?
>
> David
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