[SciPy-User] Compiling SciPy almost works

Benjamin Root ben.root@ou....
Wed Aug 4 10:08:58 CDT 2010


On Wed, Aug 4, 2010 at 6:55 AM, Søren Gammelmark <gammelmark@phys.au.dk>wrote:

> Hi everyone
>
> I just finished compiling NumPy 1.4.1 and SciPy 0.8.0 using Intel C++
> and Fortran compilers (Version 9.1) and linking to Intel MKL 10.2. SciPy
> appears to compile fine, but a couple of the modules seems to be broken.
> When I import scipy.sparse i get the following error
>
>     import scipy.sparse
>   File
> "/home/sgamark/usr/lib/python2.6/site-packages/scipy/sparse/__init__.py",
> line
> 6, in <module>
>     from csr import *
>   File
> "/home/sgamark/usr/lib/python2.6/site-packages/scipy/sparse/csr.py",
> line 12, in <module>
>     from sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \
>   File
>
> "/home/sgamark/usr/lib/python2.6/site-packages/scipy/sparse/sparsetools/__init__.py",
> line 4, in <module>
>     from csr import *
>   File
>
> "/home/sgamark/usr/lib/python2.6/site-packages/scipy/sparse/sparsetools/csr.py",
> line 7, in <module>
>     import _csr
> ImportError:
>
> /home/sgamark/usr/lib/python2.6/site-packages/scipy/sparse/sparsetools/_csr.so:
> undefined symbol: __gxx_personality_v0
>
> It is the same problem with scipy.interpolate. From what I can find out
> by googling gxx_personality, it has something to do with gcc and g++
> linking. This is odd however, since SciPy was compiled using
>
> python setup.py --compiler=intel --fcompiler=intelem
>
> Have anyone come across this problem before? (I couldn't find anything
> in the archives). Does anyone have a suggestion how to fix this?
>
> Søren Gammelmark
>

Søren,

Possibly you might have a dirty build where some stuff from your previous
attempts compiled and some stuff that didn't is now getting compiled
differently.  Try completely removing the build directory and the
numpy/scipy installs and start fresh.

Ben Root
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