[SciPy-user] installation problems on SUSE 10.2

John Schulman joschu@caltech....
Thu Jun 25 17:01:05 CDT 2009


I ran
zypper install gcc-fortran blas lapack

I installed numpy from source, it passes all tests.
I install scipy from source, and it seems to go through successfully.
But I get errors when I try to import any of the submodules of scipy.
Below I pasted what happens with test(). Maybe someone knows what I
should try.

I may give up on this and put on a new linux distro. What linux distro
is it easy to get scipy and its dependencies working?

Thanks,
John



>>> import scipy
>>> scipy.test()
Running unit tests for scipy-0.0.0-py2.5-linux-x86_64.egg.scipy
NumPy version 1.4.0.dev7073
NumPy is installed in /usr/local/lib64/python2.5/site-packages/numpy
SciPy version 0.7.1rc3
SciPy is installed in
/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy
Python version 2.5 (r25:51908, Aug  1 2008, 00:36:28) [GCC 4.1.2
20061115 (prerelease) (SUSE Linux)]
nose version 0.11.1
/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linsolve/__init__.py:4:
DeprecationWarning: scipy.linsolve has moved to
scipy.sparse.linalg.dsolve
  warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve',
DeprecationWarning)
EEEEEEEEEEEE
======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/integrate/__init__.py",
line 10, in <module>
    from odepack import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/integrate/odepack.py",
line 7, in <module>
    import _odepack
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/interpolate/__init__.py",
line 13, in <module>
    from rbf import Rbf
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/interpolate/rbf.py",
line 47, in <module>
    from scipy import linalg
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linalg/basic.py",
line 17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linalg/lapack.py",
line 17, in <module>
    from scipy.linalg import flapack
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/lib/blas/__init__.py",
line 9, in <module>
    import fblas
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/lib/lapack/__init__.py",
line 9, in <module>
    import calc_lwork
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linalg/basic.py",
line 17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linalg/lapack.py",
line 17, in <module>
    from scipy.linalg import flapack
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linsolve/__init__.py",
line 6, in <module>
    from scipy.sparse.linalg.dsolve import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/sparse/linalg/__init__.py",
line 5, in <module>
    from isolve import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/sparse/linalg/isolve/__init__.py",
line 4, in <module>
    from iterative import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/sparse/linalg/isolve/iterative.py",
line 5, in <module>
    import _iterative
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/maxentropy/__init__.py",
line 9, in <module>
    from maxentropy import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/maxentropy/maxentropy.py",
line 74, in <module>
    from scipy import optimize
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/optimize/__init__.py",
line 11, in <module>
    from lbfgsb import fmin_l_bfgs_b
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/optimize/lbfgsb.py",
line 30, in <module>
    import _lbfgsb
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/odr/__init__.py",
line 11, in <module>
    import odrpack
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/odr/odrpack.py",
line 103, in <module>
    from scipy.odr import __odrpack
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/optimize/__init__.py",
line 11, in <module>
    from lbfgsb import fmin_l_bfgs_b
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/optimize/lbfgsb.py",
line 30, in <module>
    import _lbfgsb
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/signal/__init__.py",
line 10, in <module>
    from filter_design import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/signal/filter_design.py",
line 12, in <module>
    from scipy import special, optimize
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/optimize/__init__.py",
line 11, in <module>
    from lbfgsb import fmin_l_bfgs_b
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/optimize/lbfgsb.py",
line 30, in <module>
    import _lbfgsb
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/sparse/linalg/__init__.py",
line 5, in <module>
    from isolve import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/sparse/linalg/isolve/__init__.py",
line 4, in <module>
    from iterative import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/sparse/linalg/isolve/iterative.py",
line 5, in <module>
    import _iterative
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

======================================================================
ERROR: Failure: ImportError (/usr/lib64/libblas.so.3: undefined
symbol: _gfortran_st_write_done)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/loader.py",
line 379, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib64/python2.5/site-packages/nose-0.11.1-py2.5.egg/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/stats/__init__.py",
line 7, in <module>
    from stats import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/stats/stats.py",
line 199, in <module>
    import scipy.linalg as linalg
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linalg/__init__.py",
line 8, in <module>
    from basic import *
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linalg/basic.py",
line 17, in <module>
    from lapack import get_lapack_funcs
  File "/usr/local/lib64/python2.5/site-packages/scipy-0.0.0-py2.5-linux-x86_64.egg/scipy/linalg/lapack.py",
line 17, in <module>
    from scipy.linalg import flapack
ImportError: /usr/lib64/libblas.so.3: undefined symbol: _gfortran_st_write_done

----------------------------------------------------------------------
Ran 12 tests in 0.029s

FAILED (errors=12)
<nose.result.TextTestResult run=12 errors=12 failures=0>
>>>


More information about the SciPy-user mailing list