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

Skipper Seabold jsseabold@gmail....
Thu Sep 24 12:50:43 CDT 2009


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
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