Gentoo Logo
Gentoo Spaceship




Note: Due to technical difficulties, the Archives are currently not up to date. GMANE provides an alternative service for most mailing lists.
c.f. bug 424647
List Archive: gentoo-science
Navigation:
Lists: gentoo-science: < Prev By Thread Next > < Prev By Date Next >
Headers:
To: gentoo-science@g.o
From: Marc Vinyals <marcvinyals@...>
Subject: Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
Date: Wed, 1 Jun 2011 17:48:46 +0200
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.

Best,
Marc.
Attachment:
signature.asc (PGP signature)
Replies:
Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
-- Francois Bissey
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
Navigation:
Lists: gentoo-science: < Prev By Thread Next > < Prev By Date Next >
Previous by thread:
Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
Next by thread:
Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
Previous by date:
Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
Next by date:
Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv


Updated Jul 05, 2012

Summary: Archive of the gentoo-science mailing list.

Donate to support our development efforts.

Copyright 2001-2013 Gentoo Foundation, Inc. Questions, Comments? Contact us.