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

Francis F.Drossaert@googlemail....
Tue Sep 16 04:16:46 CDT 2008


> Do you really need python 2.5 ? By building your own python, you are
> forcing yourself to build every package you will need for python,
> including the dependencies. For matplotlib, it will be painful. Python
> 2.4 is enough (incidentally, I have to use Centos 5 at some place, on
> the same architecture).

I don't really need Python2.5. Python2.4 is actually available on the
network but I think I will run into problems using the network one and
try using local libraries. I assume one would need to change the paths
on a file which I can't change. Anyway I installed Python2.5 without
any problems. I guess the problem is combining numpy/scipy with the
lapack/blas/atlas package.

> For Blas/Lapack, how did you build them ? (Which version, which
> makefile, which fortran compiler).

I forgot to include the link: http://www.scipy.org/Installing_SciPy/.
I basically followed the instructions mentioned at `building Atlas by
hand`. The build did not result in any errors. I have also tried to
build it using OPTS = -O2 -fPIC -m64 and NOOPT = -O0 -fPIC -m64 when
building the Lapack.

> > However after installing I tried to import numpy in python and
> > received to following error:  ImportError:
> > /users/francisd/local/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so:
> > undefined symbol: zgesdd_
>
> What lapack_lite.so does depend on ? (ldd
> /users/francisd/local/lib/python2.5/site-packages/numpy/linalg/lapack_lite.so)

Output:

        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b4187472000)
        libc.so.6 => /lib64/libc.so.6 (0x00002b418768c000)
        /lib64/ld-linux-x86-64.so.2 (0x00000036b8800000)

> > Googling this error, it seems that the error is caused by having a
> > wrong lapack version. I am running Centos 5 (basically Red Hat
> > Enterprise Linux 5) on a x86_64 machine.
>
> Unfortunately, it can be many things. Blas/Lapack/Atlas are difficult to
> build by yourself, there are tens of way to screw up at any point. If
> you give us the above information, it should be clearer where exactly an
> error was made

You make it sound as there is no easy solution.

> cheers,
>
> David
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