[SciPy-user] Installing scipy: getting worse..

Robert Kern robert.kern at gmail.com
Tue Jan 23 12:58:14 CST 2007


[Pre. S.: You don't have to include me on the To: line as well. I'm on the list,
and it messes up my mail filters (which admittedly are probably pretty lame).]

Eric Emsellem wrote:
> Hi,
> 
> after the trouble I had with lapack and blas, I decided to reinstall
> everything..
> Now I end up with a different (still annoying) message about libraries
> not being found.
> Here it is (and below I provide the details of what I have done to
> install everything again).
> 
> Any help is VERY welcome ....!!!
> 
> Eric
> 
> ### Doing a config on scipy gives:
> python setup.py config
> 
> Traceback (most recent call last):
>   File "setup.py", line 55, in ?
>     setup_package()
>   File "setup.py", line 28, in setup_package
>     from numpy.distutils.core import setup
>   File "/usr/local/lib/python2.4/site-packages/numpy/__init__.py", line
> 40, in ?
>     import linalg
>   File
> "/usr/local/lib/python2.4/site-packages/numpy/linalg/__init__.py", line
> 4, in ?
>     from linalg import *
>   File "/usr/local/lib/python2.4/site-packages/numpy/linalg/linalg.py",
> line 25, in ?
>     from numpy.linalg import lapack_lite
> ImportError:
> /usr/local/lib/python2.4/site-packages/numpy/linalg/lapack_lite.so:
> undefined symbol: ATL_cGetNB

Xavier is probably correct in his assessment why you get this error. However, it
looks like you built ATLAS after numpy which is odd.

Make sure that you build ATLAS first. You're putting it in /usr/local/lib/atlas/
which is fine.

Now, make a site.cfg file with the right information.


# The order of the libraries is important! Don't change them!
[blas_opt]
library_dirs = /usr/local/lib/atlas/
libraries = f77blas, cblas, atlas

[lapack_opt]
library_dirs = /usr/local/lib/atlas/
libraries = lapack, f77blas, cblas, atlas


Now build numpy. Put the site.cfg file next to the setup.py file in the root of
your checkout directory. The install should go smoothly. Run the test suite to
make sure.

  $ python -c "import numpy; numpy.test()"

Now build scipy. Again, put the site.cfg file next to the setup.py file in the
root of your checkout directory. The install should also go smoothly. Run the
test suite to make sure.

  $ python -c "import scipy; scipy.test()"

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth."
  -- Umberto Eco


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