[SciPy-dev] Scipy Compile and Testing Problem from SVN

Skipper Seabold jsseabold@gmail....
Fri Apr 10 20:42:35 CDT 2009


Hello all,

I am having some trouble compiling the development versions of Scipy
and Numpy from SVN and then getting the tests to run without errors.
>From the errors I've seen and having combed the archives, I wonder if
it's a compiler issue (gnu95 4.3.2).  Or most likely some other user
error...  So far I have tried to avoid installing ATLAS and LAPACK
from source.

I am using openSUSE 11.1 (32-bit), Python 2.6, and the most recent
version of scipy and numpy from SVN.  I have installed the following
all from the openSUSE repo openSUSE_Education

libatlas3
libatlas3-devel
blas
libblas3
libumfpack5_2_0
umfpack-devel
lapack
liblapack3
fftw
fftw-devel
fftw3
fftw3-devel
fftw3-threads
amd
amd-devel
libamd2_2_0

For both Numpy and Scipy, I edited the site.cfg as I discovered was
necessary after a first go around.

[DEFAULT]
library_dirs = /usr/local/lib:/usr/lib
include_dirs = /usr/local/include:/usr/include:/usr/include/suitesparse

And uncommented blas, lapack (not the pthreads), amd, umfpack, fftw

I then ran for numpy

~>python setup.py build --help-fcompiler
Says that gnu95 (4.3.2) is found
~>python setup.py build --fcompiler=gnu95
~>sudo python setup.py install --prefix="/usr"

For Scipy
~>python setup.py build --fcompiler=gnu95
~>sudo python setup.py install --prefix="/usr"

Both install without any errors.

Tests go as follows

>>> np.test()
...
Ran 2036 tests in 10.726s

OK (KNOWNFAIL=1)
<nose.result.TextTestResult run=2036 errors=0 failures=0>

>>> sp.test()
Running unit tests for scipy
NumPy version 1.4.0.dev6859
NumPy is installed in /usr/lib/python2.6/site-packages/numpy
SciPy version 0.8.0.dev5655
SciPy is installed in /usr/lib/python2.6/site-packages/scipy
Python version 2.6 (r26:66714, Feb  3 2009, 20:52:03) [GCC 4.3.2
[gcc-4_3-branch revision 141291]]
nose version 0.10.4
......................................................................................................................................................................................................................................................................E.........................................................../usr/lib/python2.6/site-packages/scipy/io/matlab/tests/test_mio.py:437:
FutureWarning: Using oned_as default value ('column') This will change
to 'row' in future versions
  mfw = MatFile5Writer(StringIO())
......../usr/lib/python2.6/site-packages/scipy/io/matlab/mio.py:84:
FutureWarning: Using struct_as_record default value (False) This will
change to True in future versions
  return MatFile5Reader(byte_stream, **kwargs)
.............Warning: 1000000 bytes requested, 20 bytes read.
./usr/lib/python2.6/site-packages/numpy/lib/utils.py:108:
DeprecationWarning: write_array is deprecated
  warnings.warn(str1, DeprecationWarning)
/usr/lib/python2.6/site-packages/numpy/lib/utils.py:108:
DeprecationWarning: read_array is deprecated
  warnings.warn(str1, DeprecationWarning)
..E..................../usr/lib/python2.6/site-packages/numpy/lib/utils.py:108:
DeprecationWarning: npfile is deprecated
  warnings.warn(str1, DeprecationWarning)
.........................................................................................................................................................EEE....................................................................................................................................................................................................................................................................................................................................................................................................................................E......................................E..../usr/lib/python2.6/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:143:
DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be
removed, install scikits.umfpack instead
  ' install scikits.umfpack instead', DeprecationWarning )
../usr/lib/python2.6/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:78:
DeprecationWarning: scipy.sparse.linalg.dsolve.umfpack will be
removed, install scikits.umfpack instead
  ' install scikits.umfpack instead', DeprecationWarning )
.....E.......EE............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................E...........................................................warning:
specified build_dir '_bad_path_' does not exist or is not writable.
Trying default locations
...warning: specified build_dir '..' does not exist or is not
writable. Trying default locations
..warning: specified build_dir '_bad_path_' does not exist or is not
writable. Trying default locations
...warning: specified build_dir '..' does not exist or is not
writable. Trying default locations
............................building extensions here:
/home/skipper/.python26_compiled/m30
................................................................................................
======================================================================
ERROR: Failure: ImportError
(/usr/lib/python2.6/site-packages/scipy/linalg/clapack.so: undefined
symbol: clapack_sgesv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.6/site-packages/scipy/interpolate/__init__.py",
line 13, in <module>
    from rbf import Rbf
  File "/usr/lib/python2.6/site-packages/scipy/interpolate/rbf.py",
line 47, in <module>
    from scipy import linalg
  File "/usr/lib/python2.6/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line
17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.6/site-packages/scipy/linalg/lapack.py", line
18, in <module>
    from scipy.linalg import clapack
ImportError: /usr/lib/python2.6/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv

======================================================================
ERROR: test_integer (test_array_import.TestReadArray)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/scipy/io/tests/test_array_import.py",
line 52, in test_integer
    from scipy import stats
  File "/usr/lib/python2.6/site-packages/scipy/stats/__init__.py",
line 7, in <module>
    from stats import *
  File "/usr/lib/python2.6/site-packages/scipy/stats/stats.py", line
199, in <module>
    import scipy.linalg as linalg
  File "/usr/lib/python2.6/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line
17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.6/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/python2.6/site-packages/scipy/lib/lapack/clapack.so:
undefined symbol: clapack_sgesv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.6/site-packages/scipy/lib/lapack/__init__.py",
line 16, in <module>
    import clapack
ImportError: /usr/lib/python2.6/site-packages/scipy/lib/lapack/clapack.so:
undefined symbol: clapack_sgesv

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.6/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line
17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.6/site-packages/scipy/linalg/lapack.py", line
17, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.6/site-packages/scipy/maxentropy/__init__.py",
line 9, in <module>
    from maxentropy import *
  File "/usr/lib/python2.6/site-packages/scipy/maxentropy/maxentropy.py",
line 75, in <module>
    from scipy.linalg import norm
  File "/usr/lib/python2.6/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line
17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.6/site-packages/scipy/linalg/lapack.py", line
17, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: test_implicit (test_odr.TestODR)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/scipy/odr/tests/test_odr.py",
line 88, in test_implicit
    out = implicit_odr.run()
  File "/usr/lib/python2.6/site-packages/scipy/odr/odrpack.py", line
1055, in run
    self.output = Output(apply(odr, args, kwds))
TypeError: y must be a sequence or integer (if model is implicit)

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.6/site-packages/scipy/signal/__init__.py",
line 11, in <module>
    from ltisys import *
  File "/usr/lib/python2.6/site-packages/scipy/signal/ltisys.py", line
9, in <module>
    import scipy.interpolate as interpolate
  File "/usr/lib/python2.6/site-packages/scipy/interpolate/__init__.py",
line 13, in <module>
    from rbf import Rbf
  File "/usr/lib/python2.6/site-packages/scipy/interpolate/rbf.py",
line 47, in <module>
    from scipy import linalg
  File "/usr/lib/python2.6/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line
17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.6/site-packages/scipy/linalg/lapack.py", line
17, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.6/site-packages/scipy/sparse/linalg/dsolve/tests/test_linsolve.py",
line 6, in <module>
    from scipy.linalg import norm, inv
  File "/usr/lib/python2.6/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line
17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.6/site-packages/scipy/linalg/lapack.py", line
17, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.6/site-packages/scipy/sparse/linalg/eigen/lobpcg/tests/test_lobpcg.py",
line 8, in <module>
    from scipy import arange, ones, rand, set_printoptions, r_, diag,
linalg
  File "/usr/lib/python2.6/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line
17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.6/site-packages/scipy/linalg/lapack.py", line
17, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.6/site-packages/scipy/sparse/linalg/isolve/tests/test_iterative.py",
line 8, in <module>
    from scipy.linalg import norm
  File "/usr/lib/python2.6/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line
17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.6/site-packages/scipy/linalg/lapack.py", line
17, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/loader.py",
line 364, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python2.6/site-packages/nose-0.10.4-py2.6.egg/nose/importer.py",
line 84, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python2.6/site-packages/scipy/stats/__init__.py",
line 7, in <module>
    from stats import *
  File "/usr/lib/python2.6/site-packages/scipy/stats/stats.py", line
199, in <module>
    import scipy.linalg as linalg
  File "/usr/lib/python2.6/site-packages/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/lib/python2.6/site-packages/scipy/linalg/basic.py", line
17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/lib/python2.6/site-packages/scipy/linalg/lapack.py", line
17, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

----------------------------------------------------------------------
Ran 2216 tests in 24.603s

FAILED (errors=11)
<nose.result.TextTestResult run=2216 errors=11 failures=0>

---

Some more possibly useful output (though I'm not quite sure I see any
problem here):

skipper@linux:/usr/lib/python2.6/site-packages/scipy/linalg> ldd flapack.so
        linux-gate.so.1 =>  (0xffffe000)
        /usr/lib/libv4l/v4l2convert.so (0xb8056000)
        liblapack.so.3 => /usr/lib/liblapack.so.3 (0xb77f9000)
        libf77blas.so => /usr/lib/libf77blas.so (0xb77d8000)
        libcblas.so => /usr/lib/libcblas.so (0xb77b6000)
        libatlas.so => /usr/lib/libatlas.so (0xb712e000)
        libpython2.6.so.1.0 => /usr/lib/libpython2.6.so.1.0 (0xb6fc0000)
        libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0xb6f05000)
        libm.so.6 => /lib/libm.so.6 (0xb6edc000)
        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb6ecd000)
        libc.so.6 => /lib/libc.so.6 (0xb6d71000)
        libv4l2.so.0 => /usr/lib/libv4l2.so.0 (0xb6d66000)
        libblas.so.3 => /usr/lib/libblas.so.3 (0xb6cb8000)
        libpthread.so.0 => /lib/libpthread.so.0 (0xb6c9e000)
        libdl.so.2 => /lib/libdl.so.2 (0xb6c99000)
        libutil.so.1 => /lib/libutil.so.1 (0xb6c95000)
        /lib/ld-linux.so.2 (0xb80c9000)
        libv4lconvert.so.0 => /usr/lib/libv4lconvert.so.0 (0xb6c2e000)

skipper@linux:/usr/lib/python2.6/site-packages/scipy/linalg> ldd clapack.so
        linux-gate.so.1 =>  (0xffffe000)
        /usr/lib/libv4l/v4l2convert.so (0xb8083000)
        liblapack.so.3 => /usr/lib/liblapack.so.3 (0xb7826000)
        libf77blas.so => /usr/lib/libf77blas.so (0xb7805000)
        libcblas.so => /usr/lib/libcblas.so (0xb77e3000)
        libatlas.so => /usr/lib/libatlas.so (0xb715b000)
        libpython2.6.so.1.0 => /usr/lib/libpython2.6.so.1.0 (0xb6fed000)
        libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0xb6f32000)
        libm.so.6 => /lib/libm.so.6 (0xb6f09000)
        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb6efa000)
        libc.so.6 => /lib/libc.so.6 (0xb6d9e000)
        libv4l2.so.0 => /usr/lib/libv4l2.so.0 (0xb6d93000)
        libblas.so.3 => /usr/lib/libblas.so.3 (0xb6ce5000)
        libpthread.so.0 => /lib/libpthread.so.0 (0xb6ccb000)
        libdl.so.2 => /lib/libdl.so.2 (0xb6cc6000)
        libutil.so.1 => /lib/libutil.so.1 (0xb6cc2000)
        /lib/ld-linux.so.2 (0xb80a4000)
        libv4lconvert.so.0 => /usr/lib/libv4lconvert.so.0 (0xb6c5b000)

Any help or advice would be much appreciated.  I can provide anymore
information that would be useful.

Cheers,

Skipper


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