[Numpy-discussion] building numpy locally but get error: undefined symbol: zgesdd_

Francis F.Drossaert@googlemail....
Tue Sep 16 11:59:57 CDT 2008


On 16 Sep, 16:13, David Cournapeau <da...@ar.media.kyoto-u.ac.jp>
wrote:
> Francis wrote:
> > You are right. I have recompiled everything with gfortran, but now I
> > get the following error when I try to import numpy: undefined symbol:
> > _gfortran_concat_string.
>
> This means something at some point was not built with gfortran, or that
> you did not use gfortran to build numpy. Which .so file generates this
> error ? Can you give us the result of ldd on that .so ?

To be frank, I am bit of noob, but not completely. I use the gfortran
make.inc to build lapack. The make.inc file to build and install atlas
is using gfortran.  I used the --fcompiler=gfortran flag. I don't
think there is much else I can do.

> Also, are you sure libraries paths are correctly propagated ? In
> particular, you should have LD_LIBRARY_PATH set up correctly to where
> you put your bustom-built libraries.

Being a noob, I just followed the instructions on
http://www.scipy.org/Installing_SciPy/Linux.

> > I have build a while ago sage-math (where everything is build
> > locally), but I delete it since it was over 1GB and I am only
> > interested in numpy+scipy+sympy+matlibplot. Although I did not test it
> > extensive, importing numpy and scipy was not a problem.
>
> Yes, I think they package everything by themselves. I am starting to
> think that we should do the same for blas/lapack, that's also how R does
> it by default, and I am so tired of seeing the same errors coming again
> and again. I think that distributions will never package blas/lapack
> correctly, it is hopeless.
>
> You could also try EPD,

Unfortunately there is no EPD installer for Centos 5 version. There
was a blog how to install it, but that look a lot more complicated
than what I am trying now.

I will try to build sage and look if I can build numpy against the
atlas libraries in sage. Otherwise I use sage and remove all the
packages that are not relevant for me, e.g. maxima, gap, singular,
etc.


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