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To: gentoo-science@g.o
From: Marc Vinyals <marcvinyals@...>
Subject: Re: sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
Date: Thu, 2 Jun 2011 12:32:50 +0200
EL Thu, 2 Jun 2011 07:22:18 +1200
Francois Bissey <fbissey@...> escrigué:

> > 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
> 

Here are my logs. You'll find some warnings in the configuration
stage, I hope they'll mean something to you. Also, there's no trace of
libclapack.so in
ldd /usr/lib64/python2.7/site-packages/scipy/linalg/clapack.so.
Attachment:
dev-python:numpy-1.6.0:20110602-095859.log.bz2 (application/bzip)
Attachment:
sci-libs:scipy-0.9.0-r1:20110602-100122.log.bz2 (application/bzip)
Attachment:
ldd-clapack (Binary data)
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
Re: 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
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Updated Jul 05, 2012

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