scipy: clapack.so: undefined symbol: clapack_sgesv

[petr2008]

Hi,

I have installed new gentoo linux and I am getting strange error
with scipy.

scipy version: sci-libs/scipy-0.9.0-r1 USE="-doc -umfpack"

Example script:

#! /usr/bin/env python
# -*- coding: utf-8 -*-
import scipy.interpolate as scii
xwf=1.0
lx = [ 1,2,3,4,5]
ly = [ 5,2,1,2,5]
spline = scii.UnivariateSpline(lx, ly, k=3, s=float(len(ly))*xwf)
lxs = [ 1.5,2.5,3.5]
lys = spline(lxs)
print lys

it gives me:

python testscipy.py
Traceback (most recent call last):
File "testscipy.py", line 3, in <module>
import scipy.interpolate as scii
File "/usr/lib64/python2.7/site-packages/scipy/interpolate/__init__.py", line 13, in <module>
from rbf import Rbf
File "/usr/lib64/python2.7/site-packages/scipy/interpolate/rbf.py", line 48, in <module>
from scipy import linalg
File "/usr/lib64/python2.7/site-packages/scipy/linalg/__init__.py", line 9, in <module>
from basic import *
File "/usr/lib64/python2.7/site-packages/scipy/linalg/basic.py", line 14, in <module>
from lapack import get_lapack_funcs
File "/usr/lib64/python2.7/site-packages/scipy/linalg/lapack.py", line 15, in <module>
from scipy.linalg import clapack
ImportError: /usr/lib64/python2.7/site-packages/scipy/linalg/clapack.so: undefined symbol: clapack_sgesv

On another machine it works ok.
I am not able to figure out the difference in configuration.
Well, /usr/lib64/python2.7/site-packages/scipy/linalg/clapack.so files differ.

Thank for any hint,

Petr


ps:
old machine (scipy works):
eix -s scipy
sci-libs/scipy
Available versions: 0.8.0!t ~0.9.0!t 0.9.0-r1 ~0.9.0-r2 {doc umfpack}
Installed versions: 0.9.0-r1!t(10:41:41 16/05/11)(-doc -umfpack)

new machine (scipy does not work):
eix -s scipy
sci-libs/scipy
Available versions: 0.8.0!t ~0.9.0!t 0.9.0-r1 ~0.9.0-r2 {doc umfpack}
Installed versions: 0.9.0-r1(09:51:58 10/13/11)(-doc -umfpack)

[mark_alec]

Try scipy-0.9.0-r2 - it has a patch to fix this.

[petr2008]

With scipy (~)0.9.0-r2 the problem persists.
Mayby I have chosen wrong profile to build the system:

eselect profile list

[7] default/linux/amd64/10.0/server *

I am sitting behid the firewall so I do not want to bother with security.
Default make.conf contained :
USE="mmx sse sse2"
I left it there. I think these flags have no meaning on amd64.

Petr

[big_gie]

Also of interest: http://einstein.drexel.edu/~wking/unfol ... and_ATLAS/
I'm trying it right now...

[petr2008]

Also of interest: http://einstein.drexel.edu/~wking/unfol ... and_ATLAS/
I'm trying it right now...

problem solved, thanks
petr