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POscipy gives undefined symbol: clapack_sgesv
 

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  1. POscipy gives undefined symbol: clapack_sgesv
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    <p>I want to have a clean start so I've compiled my own copies of the latest ATLAS, Lapack, and Python 2.7.3.</p> <p>I've installed numpy and it recoginizes the BLAS from ATLAS and the following works ...</p> <pre><code> python import numpy numpy.test() </code></pre> <p>But scipy is not so easy!</p> <pre><code>$ python Python 2.7.3 (default, Jan 14 2013, 13:13:35) [GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux2 Type "help", "copyright", "credits" or "license" for more information. &gt;&gt;&gt; import scipy.linalg Traceback (most recent call last): File "&lt;stdin&gt;", line 1, in &lt;module&gt; File "/projects/nrel/cid/ladab/pkgi/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 133, in &lt;module&gt; from basic import * File "/projects/nrel/cid/ladab/pkgi/lib/python2.7/site-packages/scipy/linalg/basic.py", line 12, in &lt;module&gt; from lapack import get_lapack_funcs File "/projects/nrel/cid/ladab/pkgi/lib/python2.7/site-packages/scipy/linalg/lapack.py", line 15, in &lt;module&gt; from scipy.linalg import clapack ImportError: /projects/nrel/cid/ladab/pkgi/lib/python2.7/site-packages/scipy/linalg/clapack.so: undefined symbol: +clapack_sgesv $ which python /projects/nrel/cid/ladab/pkgi/bin/python $ ldd /projects/nrel/cid/ladab/pkgi/lib/python2.7/site-packages/scipy/linalg/clapack.so linux-vdso.so.1 =&gt; (0x00007fff57bff000) libgfortran.so.3 =&gt; /usr/lib64/libgfortran.so.3 (0x00007f9229192000) libm.so.6 =&gt; /lib64/libm.so.6 (0x00007f9228ef4000) libgcc_s.so.1 =&gt; /lib64/libgcc_s.so.1 (0x00007f9228cde000) libc.so.6 =&gt; /lib64/libc.so.6 (0x00007f922894b000) /lib64/ld-linux-x86-64.so.2 (0x000000387dc00000) $ cat scipy-0.11.0/site.cfg [DEFAULT] library_dirs = /projects/nrel/cid/ladab/pkgi/lib include_dirs = /projects/nrel/cid/ladab/pkgi/include [blas_opt] libraries = f77blas, cblas, atlas [lapack_opt] libraries = lapack, f77blas, cblas, atlas $ env | egrep python PYTHONPATH=/projects/nrel/cid/ladab/pkgi/lib/python2.7/site-packages </code></pre> <p>Searching for a definition of clapack_sgesv, I find none in the site-packages/scipy:</p> <pre><code>$ cd /projects/nrel/cid/ladab/pkgi/lib/python2.7/site-packages/scipy/linalg $ for ii in *.so; do echo ========== $ii; nm $ii | egrep clapack_sgesv &gt; done ========== atlas_version.so ========== calc_lwork.so ========== cblas.so ========== clapack.so U clapack_sgesv 00000000002103e0 d doc_f2py_rout_clapack_sgesv 0000000000009810 t f2py_rout_clapack_sgesv ========== fblas.so ========== flapack.so ========== _flinalg.so </code></pre> <p>It is apparently available at the LD_LIBRARY_PATH, but scipy isn't using it ...</p> <pre><code>$ echo $LD_LIBRARY_PATH /projects/nrel/cid/ladab/pkgi/lib:/usr/lib64 $ cd /projects/nrel/cid/ladab/pkgi/lib $ for ii in *.so; do echo ========== $ii; nm $ii | egrep clapack_sgesv; done ========== libsatlas.so 0000000000094ce0 T clapack_sgesv ========== libtatlas.so 00000000000accb0 T clapack_sgesv </code></pre> <p>Do you have any suggestions?</p>
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    1. PTQuestion
    1. USAdam Cadien
    1. USSullivan
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    1. COScipy provides pretty detailed instructions, http://www.scipy.org/Installing_SciPy/Linux, unless your system is heavily customized I've found these to work without fail. I hope that helps.
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      1. POscipy gives undefined symbol: clapack_sgesv
      1. USAdam Cadien
 

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