[Numpy-discussion] building numpy against Cray xt-libsci

[Charles R Harris]

On Mon, May 24, 2010 at 1:57 AM, Amir <amirnntp at gmail.com> wrote:

> I am trying to build numpy against Cray's xt-libsci library on a Cray XT5.
> I am getting an error I am hoping for hints on how to resolve:
>
> In [1]: import numpy
> <snip>
>      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: /opt/xt-libsci/10.4.0/gnu/lib/libsci.so: undefined symbol:
> fftw_version
>
> These are the symbols in libsci:
>
> %  nm /opt/xt-libsci/10.4.0/gnu/lib/libsci.so | grep fftw_version
> 00000000010f9a30 B __crafft_internal__crafft_fftw_version_num
>                  U fftw_version
> 00000000005aa8a4 T get_fftw_version
>
>
> I first built numpy with no custom site.cfg file. It built correctly and
> all tests ran. But it was too slow.
>
> Then I tried building numpy against libsci, which has BLAS, LAPACK, FFTW3
> among other things. I had to build a libcblas.a from the netlib src as
> libsci does not have cblas (using gcc, gfortran 4.3.3). Here is my site.cfg,
> accumulated from several nice tutorials on how to build numpy on these
> machines, which for some reason don't work for me. The instructions were
> based on numpy 1.2.
>
> [blas]
> blas_libs = cblas
> library_dirs = /global/homes/amir/local/lib
>
> [lapack]
> lapack_libs = sci
> library_dirs = /opt/xt-libsci/10.4.0/gnu/lib
>
> [blas_opt]
> blas_libs = cblas, sci
> libraries = cblas, sci
>
> [lapack_opt]
> libraries = sci
>
> [fftw]
> libraries = fftw3
>
>
> Here is what is linked to lapack_lite.so:
>
> % ldd ./numpy/linalg/lapack_lite.so
> libsci.so => /opt/xt-libsci/10.4.0/gnu/lib/libsci.so (0x00002b4493325000)
>  libgfortran.so.3 => /opt/gcc/4.3.3/snos/lib64/libgfortran.so.3
> (0x00002b44a4579000)
> libm.so.6 => /lib64/libm.so.6 (0x00002b44a4770000)
>  libgcc_s.so.1 => /opt/gcc/4.3.3/snos/lib64/libgcc_s.so.1
> (0x00002b44a48c6000)
> libc.so.6 => /lib64/libc.so.6 (0x00002b44a49dd000)
>  /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)
>
>
Curious, fftw shows up in numpy/distutils/system_info.py and f2py, but I
think numpy/scipy no longer support fftw. Maybe we should get rid of the
references? In any case, you can probably modify
numpy/distutils/system_info.py to fix this problem, as it doesn't seem to
show up on other systems.

Chuck
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