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: Wed, 01 Jun 2011 19:23:15
Message-Id: 201106020722.18860.fbissey@slingshot.co.nz
In Reply to: Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv by Marc Vinyals
> 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. >
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

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