[ase-users] Install Error
Jens Jørgen Mortensen
jensj at fysik.dtu.dk
Fri Dec 9 10:27:16 CET 2016
Den 09-12-2016 kl. 03:35 skrev Min Gao via ase-users:
> 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 ?
Looks like some kind of scipy problem. I don't remember anyone ever
using ASE with Python 3.3, so I would recommend that you use 2.7, 3.4 or
3.5.
Jens Jørgen
> 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
> <http://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
> <http://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
> <http://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
> <http://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
> <http://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
> <http://flapack.cpython-33m.so>: undefined symbol: ilaver_
>
> ----------------------------------------------------------------------
> Ran 177 tests in 134.395s
>
> FAILED (errors=9)
>
>
>
> Sincerely Yours,
>
> Min GAO
>
> Hokkaido University
>
>
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
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