[SciPy-dev] Installing Numpy/Scipy with custom ATLAS

Skipper Seabold jsseabold@gmail....
Thu Sep 24 13:10:24 CDT 2009


On Thu, Sep 24, 2009 at 1:50 PM, Skipper Seabold <jsseabold@gmail.com> wrote:
> For some reason I thought it would be a good idea to install a custom
> ATLAS...again.
>
> I think I've built lapack 3.1.1 and atlas 3.8.0 correctly following
> the instructions here <http://www.scipy.org/Installing_SciPy/Linux>
> and the ones included with atlas, but we shall see...the checks pass
> at least.  I installed the atlas libraries to ~/atlas and copied over
> the dynamic libraries by hand.
>
> I then edit my site.cfg
>
> [DEFAULT]
> library_dirs = /usr/local/lib:/usr/lib:/home/skipper/atlas/lib
> include_dirs = /usr/local/include:/usr/include:usr/include/suitesparse:/home/skipper/atlas/include
> [blas_opt]
> libraries = ptf77blas, ptcblas, atlas
> [lapack_opt]
> libraries = lapack, ptf77blas, ptcblas, atlas
> [amd]
> amd_libs = amd
> [umfpack]
> umfpack_libs = umfpack
> [fftw]
> libraries = fftw3
>
> I then build and install numpy without error.  But when I try to
> import numpy I get
> [...]
> /usr/local/lib/python2.6/dist-packages/numpy/linalg/linalg.py in <module>()
>     20         isfinite, size
>     21 from numpy.lib import triu
> ---> 22 from numpy.linalg import lapack_lite
>     23 from numpy.matrixlib.defmatrix import matrix_power
>     24
>
> ImportError: /usr/local/lib/python2.6/dist-packages/numpy/linalg/lapack_lite.so:
> undefined symbol: ATL_dptsyrk
>
>
> Running ldd gives
>
> $ ldd /usr/local/lib/python2.6/dist-packages/numpy/linalg/lapack_lite.so
>        linux-vdso.so.1 =>  (0x00007fff129fe000)
>        liblapack.so => /usr/lib/atlas/liblapack.so (0x00007f4609c57000)
>        libatlas.so => /usr/lib/libatlas.so (0x00007f4609615000)
>        libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f4609338000)
>        libm.so.6 => /lib/libm.so.6 (0x00007f46090b3000)
>        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f4608e9b000)
>        libc.so.6 => /lib/libc.so.6 (0x00007f4608b28000)
>        libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f46084ad000)
>        /lib64/ld-linux-x86-64.so.2 (0x00007f460a991000)
>
> I currently have atlas installed from David's repo as well
> (incidentally, David, where is your repo, I can't find it again, and
> wanted to add it to the wiki.) and am wondering if there is a conflict
> here.  When I look at the build log it says, for example,
>
>  FOUND:
>    libraries = ['ptf77blas', 'ptcblas', 'atlas']
>    library_dirs = ['/home/skipper/atlas/lib']
>    language = c
>    include_dirs = ['/usr/include']
>
> Should include_dirs be '/home/skipper/atlas/include' ?  I don't know.
> Any pointers would be appreciated, as I wasn't able to install numpy
> without trying to use the threaded libraries either now...  I can
> provide anymore output as needed.  Build log attached.
>
> Cheers,
>
> Skipper
>

I figured the include directories in site.cfg were greedy, so I
changed the order to

library_dirs = /usr/local/lib:/usr/lib:/home/skipper/atlas/lib
include_dirs = /home/skipper/atlas/include:/usr/local/include:/usr/include:/usr/include/suitesparse

but I get the same import error in numpy.

The correct include directory is listed in the build log, but I'm
wondering why it says atlas 3.8.3 when I installed 3.8.0

New build log attached.

Skipper
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