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

josef.pktd@gmai... josef.pktd@gmai...
Fri Apr 10 22:21:27 CDT 2009


On Fri, Apr 10, 2009 at 9:42 PM, Skipper Seabold <jsseabold@gmail.com> wrote:
> 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


If I interpret Davids usually explanations and your logs correctly
then you are mixing fortran compilers, lapack is using gfortran and
you are using g95, which showed up pretty often on the mailing lists.

But this is just pattern recognition, I don't know anything about opensuse.

Josef


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