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To: gentoo-science@g.o
From: Francois Bissey <fbissey@...>
Subject: Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
Date: Thu, 2 Jun 2011 07:22:18 +1200
> EL Wed, 1 Jun 2011 06:57:03 +1200
> 
> Francois Bissey <fbissey@...> 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.
> 
Hi Marc,

I have been using bicatali's overlay for a bit and I recompiled all the 
cblas/lapack stack from sage a few times with different implementations
in the last few days. The only time i had an issue was when the value
eselected was not what I wanted by accident.

I am curious to see your build log for numpy and scipy. Also what does 
ldd /usr/lib64/python2.7/site-packages/scipy/linalg/clapack.so
reports?

Francois


Replies:
Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
-- Marc Vinyals
References:
sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
-- Marc Vinyals
Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
-- Francois Bissey
Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
-- Marc Vinyals
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Updated Jul 05, 2012

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