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: Thu, 02 Jun 2011 10:33:42
Message-Id: 20110602123250.57b5071c@pcbox-marc
In Reply to: Re: [gentoo-science] sci-libs/scipy-0.9.0-r1 undefined symbol: clapack_sgesv by Francois Bissey
EL Thu, 2 Jun 2011 07:22:18 +1200
Francois Bissey <fbissey@××××××××××××.nz> escrigué:

> > 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 >
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.

Attachments

File name MIME type
dev-python:numpy-1.6.0:20110602-095859.log.bz2 application/x-bzip
sci-libs:scipy-0.9.0-r1:20110602-100122.log.bz2 application/x-bzip
ldd-clapack application/octet-stream
signature.asc application/pgp-signature

Replies

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