On Mon, May 24, 2010 at 1:57 AM, Amir <[email protected]> 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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