Gentoo Archives: gentoo-science

From: Francois Bissey <fbissey@××××××××××××.nz>
To: gentoo-science@l.g.o
Subject: Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv
Date: Tue, 31 May 2011 18:58:18
Message-Id: 201106010657.03824.fbissey@slingshot.co.nz
In Reply to: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv by Marc Vinyals
> 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

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Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv Marc Vinyals <marcvinyals@××××××××.com>