Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv

[Marc Vinyals]

EL Wed, 1 Jun 2011 06:57:03 +1200
Francois Bissey <fbissey@××××××××××××.nz> escrigué:

> > Hi,
> >
> > While updating sage and python to 4.7 and 2.7, I hit a variation of
> > an old bug (see http://bugs.gentoo.org/195619): scipy compiles with
> > lapack-reference but is unusable. Running in python
> >
> > import scipy.optimize
> >
> > fails with
> >
> > [...]
> >     from scipy.linalg import clapack
> > ImportError: /usr/lib64/python2.7/site-packages/scipy/linalg/clapack.so:
> > undefined symbol: clapack_sgesv
> >
> > I tried rebuilding numpy and scipy with lapack provided (eselect) by
> > lapack-reference, blas provided by blas-reference, cblas provided by
> > gsl and with/without clapack with the same result.
> >
> > Then I tried rebuilding numpy and scipy with lapack, blas and cblas
> > provided (eselect) by atlas and scipy worked flawlessly.
> >
> > Should scipy depend on a specific lapack provider instead of a
> > virtual? Enable it at compile time? Is it an unfortunate
> > combination what fails?
> >
> > I can provide build logs if you need them.
> >
> Hi Marc,
>
> Just one thing that I can think of on the top of my head. We recently
> made scipy depend on arpack and superlu. They also have dependencies
> on blas/lapack if you didn't rebuild them as well they may cause
> trouble.
>
> I had a similar problem recently but eselecting everything properly
> worked for me. A last piece of info you could provide: are you using
> the main tree implementation or bicatali's overlay implementation?
>
> Francois
>

Hi Francois,

I tried rebuilding arpack and superlu without luck. Since you mentioned
that eselect fixed your problems, I also tried installing
cblas-reference and using it instead of gsl, also without luck.

I'm using the main tree implementation.

Best,
Marc.