[SciPy-dev] scipy compile problems

Nate twentypoundtrout@yahoo....
Sun Aug 3 17:08:23 CDT 2008


I'm having trouble compiling scipy from the repo on Ubuntu (8.04).  See the
following output error from scipy.test().  Apparently there are problems with
lapack.  I've compiled ATLAS (first building and linking the full NA lib lapack)
and still have the following errors.  The build + site-package directories for
numpy/scipy are removed each time I try to rebuild (both).  Also, I am building
everything with gfortran (following the steps here:
http://www.scipy.org/Installing_SciPy/Linux#head-1c4018a51422706809ee96a4db03ca0669f5f6d1)

Any ideas?

Nate



Here is my site.cfg file:
[DEFAULT]
library_dirs = /usr/local/atlas/lib
include_dirs = /usr/local/atlas/include

[atlas]
atlas_libs = lapack, f77blas, cblas, atlas

[amd]
library_dirs = /usr/lib
include_dirs = /usr/include/suitesparse
amd_libs = amd

[umfpack]
library_dirs = /usr/lib
include_dirs = /usr/include/suitesparse
umfpack_libs = umfpack




======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/nose-0.10.3-py2.5.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File
"/usr/lib/python2.5/site-packages/nose-0.10.3-py2.5.egg/nose/importer.py", line
39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/usr/lib/python2.5/site-packages/nose-0.10.3-py2.5.egg/nose/importer.py", line
84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File
"/usr/lib/python2.5/site-packages/scipy/integrate/tests/test_integrate.py", line
9, in <module>
    from scipy.linalg import norm
  File "/usr/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in
<module>
    from basic import *
  File "/usr/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in
<module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 17, in
<module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError
(/usr/lib/python2.5/site-packages/scipy/linalg/clapack.so: undefined symbol:
clapack_sgesv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/nose-0.10.3-py2.5.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File
"/usr/lib/python2.5/site-packages/nose-0.10.3-py2.5.egg/nose/importer.py", line
39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/usr/lib/python2.5/site-packages/nose-0.10.3-py2.5.egg/nose/importer.py", line
84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.5/site-packages/scipy/interpolate/__init__.py", line 7,
in <module>
    from interpolate import *
  File "/usr/lib/python2.5/site-packages/scipy/interpolate/interpolate.py", line
13, in <module>
    import scipy.linalg as slin
  File "/usr/lib/python2.5/site-packages/scipy/linalg/__init__.py", line 8, in
<module>
    from basic import *
  File "/usr/lib/python2.5/site-packages/scipy/linalg/basic.py", line 17, in
<module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.5/site-packages/scipy/linalg/lapack.py", line 18, in
<module>
    from scipy.linalg import clapack
ImportError: /usr/lib/python2.5/site-packages/scipy/linalg/clapack.so: undefined
symbol: clapack_sgesv



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