[SciPy-user] problem with UMFPACK in scipy.test

Robert Kern robert.kern@gmail....
Thu Apr 24 13:58:18 CDT 2008


On Thu, Apr 24, 2008 at 7:28 AM, Johann Cohen-Tanugi
<cohen@slac.stanford.edu> wrote:
> hello,
>  I have compiled and built UMFPACK, following the wiki, and when
>  configuring scipy I read :
>  umfpack_info:
>  amd_info:
>   libraries amd not found in /usr/local/lib
>   FOUND:
>     libraries = ['amd']
>     library_dirs = ['/usr/lib']
>
>   FOUND:
>     libraries = ['umfpack', 'amd']
>     library_dirs = ['/data1/sources/MATHSTUFF/UMFPACK/Lib/', '/usr/lib']
>     swig_opts = ['-I/data1/sources/MATHSTUFF/UMFPACK/Include']
>     define_macros = [('SCIPY_UMFPACK_H', None)]
>     include_dirs = ['/data1/sources/MATHSTUFF/UMFPACK/Include']
>
>  I would infer from that that UMFPACK was correctly found, but after
>  building scipy from svn, I get :

You should actually look later in the build log to see if the .so
files got linked correctly.

>  In [4]: scipy.test(verbose=2)
>  <lots of stuff>
>  ======================================================================
>  SKIP: Getting factors of complex matrix
>  ----------------------------------------------------------------------
>  Traceback (most recent call last):
>   File "/usr/lib/python2.5/site-packages/scipy/testing/decorators.py",
>  line 81, in skipper
>     raise nose.SkipTest, msg
>  SkipTest: UMFPACK appears not to be compiled
>
>  <several other outputs of the same kind>
>
>  ======================================================================
>  SKIP: Solve: single precision
>  ----------------------------------------------------------------------
>  Traceback (most recent call last):
>   File "/usr/lib/python2.5/site-packages/scipy/testing/decorators.py",
>  line 81, in skipper
>     raise nose.SkipTest, msg
>  SkipTest: UMFPACK appears not to be compiled
>
>  ----------------------------------------------------------------------
>  Ran 1524 tests in 39.269s
>
>  FAILED (failures=5, errors=12)
>
>
>  What does that mean? I noticed that when building UMFPACK I put -fPIC in
>  the UFConfig.mk but it does not seem to be honored. For instance :
>  gcc -O3 -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
>  -I../Include -I../Source -I../../AMD/Include -I../../UFconfig -DDINT -c
>  ../Source/umfpack_qsymbolic.c -o umfpack_di_qsymbolic.o
>
>  Is that related?

Quite possibly, yes.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
 -- Umberto Eco


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