Gentoo Archives: gentoo-science

From: Marc Vinyals <marcvinyals@××××××××.com>
To: gentoo-science@l.g.o
Subject: Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
Date: Wed, 01 Jun 2011 15:49:30
Message-Id: 20110601174846.5687d413@pcbox-marc
In Reply to: Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv by Francois Bissey
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.

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Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv Francois Bissey <fbissey@××××××××××××.nz>