[SciPy-user] Problem importing scipy compiled with intel compiler (/opt/intel/fc/9.0/lib/libifcore.so.5: undefined symbol: __subq)

Sourish Basu sbasu at physics.cornell.edu
Sat Nov 11 19:55:56 CST 2006


I compiled both numpy and scipy with intel compilers on a Xeon (4 cpu-s) 
which has ATLAS. It appears that numpy works fine, but scipy does not :( 
In IPython, I see the following

<interactive session>

In [1]: import numpy.linalg

In [2]: import numpy.numarray.random_array

In [3]: A = numpy.numarray.random_array.standard_normal((5,5))

In [4]: B = A + numpy.transpose(A)

In [5]: numpy.linalg.eigvals(B)
Out[5]: array([ 4.92466336, -0.25626135, -3.83930089, -2.68608889, 
-3.19828771])

In [6]: import scipy

In [7]: import scipy.linalg
---------------------------------------------------------------------------
<type 'exceptions.ImportError'>           Traceback (most recent call last)

/home/sourish/<ipython console> in <module>()

/opt/pub/lib/python2.5/site-packages/scipy/linalg/__init__.py in <module>()
      6 from linalg_version import linalg_version as __version__
      7
----> 8 from basic import *
      9 from decomp import *
     10 from matfuncs import *

/opt/pub/lib/python2.5/site-packages/scipy/linalg/basic.py in <module>()
     15 #from blas import get_blas_funcs
     16 from flinalg import get_flinalg_funcs
---> 17 from lapack import get_lapack_funcs
     18 from numpy import 
asarray,zeros,sum,newaxis,greater_equal,subtract,arange,\
     19      conjugate,ravel,r_,mgrid,take,ones,dot,transpose,sqrt,add,real

/opt/pub/lib/python2.5/site-packages/scipy/linalg/lapack.py in <module>()
     15 import numpy
     16
---> 17 from scipy.linalg import flapack
     18 from scipy.linalg import clapack
     19 _use_force_clapack = 1

<type 'exceptions.ImportError'>: /opt/intel/fc/9.0/lib/libifcore.so.5: 
undefined symbol: __subq

</interactive session>

So I can see that the linear algebra routines in numpy work fine, but 
not the ones in scipy. I compiled/installed numpy with ATLAS and Intel 
MKL libraries, defined in site.cfg, and I compiled/installed scipy with 
the command

python setup.py config_fc --fcompiler=intel config --compiler=intel 
config --cc=/opt/intel_cc_80/bin/icc install

I don't really understand what the error message means and how to fix 
it. Google wasn't much of a help. Can anyone help?

Thanks,

Sourish

P.S. - importing scipy.optimize, scipy.interpolate, or scipy.integrate 
also gives the same error.


More information about the SciPy-user mailing list