[ase-users] Install Error

[Min Gao]

Dear All

I am trying to install the ase-3.12.0 on the linux by using python3.3 and
got  several error msg. Does anyone know the reason about it ?
Thank you in advance

the initial setting is

platform        Linux-2.6.18-164.15.1.el5xen-x86_64-with-redhat-5.4-Final
python-3.3.3    /share/apps/lib/python/bin/python3.3
ase-3.12.0      /home/gaomin/ase/ase/
numpy-1.11.2    /home/gaomin/.local/lib/python3.3/site-packages/numpy/
scipy-0.18.1    /home/gaomin/.local/lib/python3.3/site-packages/scipy/
test-dir        /tmp/ase-test-6dhqjd

ERROR

atoms_get_duplicates.py ... ERROR


db.py ... Traceback (most recent call last):
  File "/home/gaomin/ase/tools/ase-build", line 3, in ?
    from ase.cli.build import main
  File "/home/gaomin/ase/ase/__init__.py", line 10, in ?
    from ase.atom import Atom
  File "/home/gaomin/ase/ase/atom.py", line 6, in ?
    from ase.utils import basestring
  File "/home/gaomin/ase/ase/utils/__init__.py", line 54
    yield
        ^
SyntaxError: invalid syntax
Traceback (most recent call last):
  File "/home/gaomin/ase/tools/ase-run", line 3, in ?
    from ase.cli.run import main
  File "/home/gaomin/ase/ase/__init__.py", line 10, in ?
    from ase.atom import Atom
  File "/home/gaomin/ase/ase/atom.py", line 6, in ?
    from ase.utils import basestring
  File "/home/gaomin/ase/ase/utils/__init__.py", line 54
    yield
        ^
SyntaxError: invalid syntax
ERROR


doctests.py ... ERROR
eam_pot.py ... ok
eam_pot_test.py ... ERROR
eam_test.py ... ERROR

eos.py ... ERROR
hcp.py ... ERROR
preconlbfgs.py ... ERROR

======================================================================
ERROR: atoms_get_duplicates.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/gaomin/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/home/gaomin/ase/ase/test/atoms_get_duplicates.py", line 10, in
<module>
    dups = get_duplicate_atoms(at)
  File "/home/gaomin/ase/ase/geometry/geometry.py", line 192, in
get_duplicate_atoms
    from scipy.spatial.distance import pdist
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/spatial/__init__.py",
line 97, in <module>
    from ._procrustes import procrustes
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/spatial/_procrustes.py",
line 11, in <module>
    from scipy.linalg import orthogonal_procrustes
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/__init__.py",
line 174, in <module>
    from .misc import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/misc.py",
line 6, in <module>
    from .lapack import get_lapack_funcs
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/lapack.py",
line 374, in <module>
    from scipy.linalg import _flapack
ImportError: /home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/_
flapack.cpython-33m.so: undefined symbol: ilaver_

======================================================================
ERROR: c60.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/gaomin/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/home/gaomin/ase/ase/test/c60.py", line 8, in <module>
    from ase.optimize.precon.neighbors import get_neighbours
  File "/home/gaomin/ase/ase/optimize/precon/__init__.py", line 33, in
<module>
    from ase.optimize.precon.precon import Precon, Exp, C1, Pfrommer, FF,
Exp_FF
  File "/home/gaomin/ase/ase/optimize/precon/precon.py", line 8, in <module>
    from scipy.sparse.linalg import spsolve
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/sparse/linalg/__init__.py",
line 112, in <module>
    from .isolve import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/
sparse/linalg/isolve/__init__.py", line 8, in <module>
    from .lgmres import lgmres
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/
sparse/linalg/isolve/lgmres.py", line 8, in <module>
    from scipy.linalg import get_blas_funcs, get_lapack_funcs, qr_insert,
lstsq
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/__init__.py",
line 174, in <module>
    from .misc import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/misc.py",
line 6, in <module>
    from .lapack import get_lapack_funcs
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/lapack.py",
line 374, in <module>
    from scipy.linalg import _flapack
ImportError: /home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/_
flapack.cpython-33m.so: undefined symbol: ilaver_

======================================================================
======================================================================
ERROR: db.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/gaomin/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/home/gaomin/ase/ase/test/db.py", line 21, in <module>
    cli(cmd.replace('y.json', name))
  File "/home/gaomin/ase/ase/test/__init__.py", line 179, in cli
    raise RuntimeError('Failed running a shell command.  '
RuntimeError: Failed running a shell command.  Please set you $PATH
environment variable!

======================================================================
ERROR: doctests.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/gaomin/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/home/gaomin/ase/ase/test/doctests.py", line 25, in <module>
    print(mod, doctest.testmod(mod, raise_on_error=True))
  File "/share/apps/lib/python/lib/python3.3/doctest.py", line 1906, in
testmod
    runner.run(test)
  File "/share/apps/lib/python/lib/python3.3/doctest.py", line 1794, in run
    r = DocTestRunner.run(self, test, compileflags, out, False)
  File "/share/apps/lib/python/lib/python3.3/doctest.py", line 1431, in run
    return self.__run(test, compileflags, out)
  File "/share/apps/lib/python/lib/python3.3/doctest.py", line 1340, in
__run
    exception)
  File "/share/apps/lib/python/lib/python3.3/doctest.py", line 1800, in
report_unexpected_exception
    raise UnexpectedException(test, example, exc_info)
doctest.UnexpectedException: <DocTest ase.build.tools.stack from
/home/gaomin/ase/ase/build/tools.py:192 (12 examples)>

======================================================================
ERROR: eam_pot_test.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/gaomin/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/home/gaomin/ase/ase/test/eam_pot_test.py", line 4, in <module>
    from ase.calculators.eam import EAM
  File "/home/gaomin/ase/ase/calculators/eam.py", line 15, in <module>
    from scipy.interpolate import InterpolatedUnivariateSpline as spline
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/interpolate/__init__.py",
line 160, in <module>
    from .interpolate import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/interpolate/interpolate.py",
line 16, in <module>
    import scipy.linalg
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/__init__.py",
line 174, in <module>
    from .misc import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/misc.py",
line 6, in <module>
    from .lapack import get_lapack_funcs
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/lapack.py",
line 374, in <module>
    from scipy.linalg import _flapack
ImportError: /home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/_
flapack.cpython-33m.so: undefined symbol: ilaver_

======================================================================
ERROR: eam_test.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/gaomin/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/home/gaomin/ase/ase/test/eam_test.py", line 3, in <module>
    from ase.calculators.eam import EAM
  File "/home/gaomin/ase/ase/calculators/eam.py", line 15, in <module>
    from scipy.interpolate import InterpolatedUnivariateSpline as spline
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/interpolate/__init__.py",
line 160, in <module>
    from .interpolate import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/interpolate/interpolate.py",
line 16, in <module>
    import scipy.linalg
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/__init__.py",
line 174, in <module>
    from .misc import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/misc.py",
line 6, in <module>
    from .lapack import get_lapack_funcs
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/lapack.py",
line 374, in <module>
    from scipy.linalg import _flapack
ImportError: /home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/_
flapack.cpython-33m.so: undefined symbol: ilaver_

======================================================================
ERROR: eos.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/gaomin/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/home/gaomin/ase/ase/test/eos.py", line 25, in <module>
    v, e, b = eos.fit()
  File "/home/gaomin/ase/ase/eos.py", line 228, in fit
    popt, pcov = curve_fit(parabola, self.v, self.e, p0)
TypeError: 'NoneType' object is not callable

======================================================================
ERROR: hcp.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/gaomin/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/home/gaomin/ase/ase/test/hcp.py", line 65, in <module>
    from scipy.optimize import fmin_bfgs
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/optimize/__init__.py",
line 233, in <module>
    from ._minimize import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/optimize/_minimize.py",
line 26, in <module>
    from ._trustregion_dogleg import _minimize_dogleg
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/
optimize/_trustregion_dogleg.py", line 5, in <module>
    import scipy.linalg
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/__init__.py",
line 174, in <module>
    from .misc import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/misc.py",
line 6, in <module>
    from .lapack import get_lapack_funcs
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/lapack.py",
line 374, in <module>
    from scipy.linalg import _flapack
ImportError: /home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/_
flapack.cpython-33m.so: undefined symbol: ilaver_

======================================================================
ERROR: preconlbfgs.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/gaomin/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/home/gaomin/ase/ase/test/preconlbfgs.py", line 5, in <module>
    from ase.optimize.precon import Exp, PreconLBFGS, PreconFIRE
  File "/home/gaomin/ase/ase/optimize/precon/__init__.py", line 33, in
<module>
    from ase.optimize.precon.precon import Precon, Exp, C1, Pfrommer, FF,
Exp_FF
  File "/home/gaomin/ase/ase/optimize/precon/precon.py", line 8, in <module>
    from scipy.sparse.linalg import spsolve
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/sparse/linalg/__init__.py",
line 112, in <module>
    from .isolve import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/
sparse/linalg/isolve/__init__.py", line 8, in <module>
    from .lgmres import lgmres
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/
sparse/linalg/isolve/lgmres.py", line 8, in <module>
    from scipy.linalg import get_blas_funcs, get_lapack_funcs, qr_insert,
lstsq
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/__init__.py",
line 174, in <module>
    from .misc import *
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/misc.py",
line 6, in <module>
    from .lapack import get_lapack_funcs
  File "/home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/lapack.py",
line 374, in <module>
    from scipy.linalg import _flapack
ImportError: /home/gaomin/.local/lib/python3.3/site-packages/scipy/linalg/_
flapack.cpython-33m.so: undefined symbol: ilaver_

----------------------------------------------------------------------
Ran 177 tests in 134.395s

FAILED (errors=9)



Sincerely Yours,

Min GAO

Hokkaido University
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