[ase-users] ASE Installation problem
Melissa A. Hines
melissa.hines at cornell.edu
Mon Oct 24 02:06:50 CEST 2016
I am trying to install ASE in a new Anaconda environment on Mac OS 10.12. Although most of the tests are passed, a few do not, as seen in the output below.
Any thoughts?
Many thanks,
Melissa
_________________________________________________
(aseNew) Shadowfax:test mah$ python -m ase.test
platform Darwin-16.0.0-x86_64-i386-64bit
python-2.7.12 /Users/mah/anaconda/envs/aseNew/bin/python
ase-3.11.0 /Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/
numpy-1.11.2 /Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/numpy/
scipy-0.18.1 /Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/scipy/
test-dir /var/folders/f5/36xgs63j2fn7yw1dzty0wd8m0000gn/T/ase-test-2iP_gQ
Ag-Cu100.py ... ok
CO2_Au111.py ... ok
COCu111_2.py ... ok
aep1.py ... ERROR
aff.py ... ok
ag.py ... ok
al.py ... ERROR
atom.py ... ok
atoms_distance.py ... ok
atoms_get_duplicates.py ... ok
atoms_info_copy.py ... ok
bader.py ... ok
bandgap.py ... ok
basin.py ... ok
build.py ... ok
bulk.py ... ok
center.py ... ok
collection.py ... ok
com.py ... ok
constr_setpos.py ... ok
coverage.py ... ok
crystal.py ... ok
db.py ... Running: H
Running: H2O
Running: O2
Running: H2
LBFGS: 0 19:51:21 1.158864 4.4619
LBFGS: 1 19:51:21 1.129374 2.9285
LBFGS: 2 19:51:21 1.072359 0.5614
LBFGS: 3 19:51:21 1.070596 0.0991
LBFGS: 4 19:51:21 1.070541 0.0026
Running: O2
LBFGS: 0 19:51:22 0.922681 3.7034
LBFGS: 1 19:51:22 0.691988 1.9589
LBFGS: 2 19:51:22 0.628304 0.5011
LBFGS: 3 19:51:22 0.624816 0.0669
LBFGS: 4 19:51:22 0.624750 0.0019
Running: Cu
Deleted 1 row
Added 9 key-value pairs (0 pairs updated)
Removed 0 key-value pairs
Added 0 key-value pairs (0 pairs updated)
Removed 3 key-value pairs
Running: H
Running: H2O
Running: O2
Running: H2
LBFGS: 0 19:51:24 1.158864 4.4619
LBFGS: 1 19:51:24 1.129374 2.9285
LBFGS: 2 19:51:24 1.072359 0.5614
LBFGS: 3 19:51:24 1.070596 0.0991
LBFGS: 4 19:51:24 1.070541 0.0026
Running: O2
LBFGS: 0 19:51:24 0.922681 3.7034
LBFGS: 1 19:51:24 0.691988 1.9589
LBFGS: 2 19:51:24 0.628304 0.5011
LBFGS: 3 19:51:24 0.624816 0.0669
LBFGS: 4 19:51:24 0.624750 0.0019
Running: Cu
Deleted 1 row
Added 9 key-value pairs (0 pairs updated)
Removed 0 key-value pairs
Added 0 key-value pairs (0 pairs updated)
Removed 3 key-value pairs
ok
db2.py ... ok
dependency_gtk.py ... ok
dependency_matplotlib.py ... ok
dihedralconstraint.py ... ok
dimer.py ... ok
dimer_method.py ... ok
distance.py ... ok
distmom.py ... ok
doctests.py ... ok
eam_test.py ... ok
emt.py ... ok
emt1.py ... ok
emt2.py ... ok
emt_h3o2m.py ... ok
eos.py ... ok
eoswoase.py ... ok
example.py ... ok
filter.py ... ok
fix_bond_length_mic.py ... ok
geometry.py ... ok
h2.py ... ok
hcp.py ... ok
hookean.py ... ok
idpp.py ... ok
maxwellboltzmann.py ... ok
md.py ... ok
mic.py ... ok
minimahop.py ... ok
mopac.py ... skipped ok
n2.py ... ok
neb.py ... ok
neb_tr.py ... ok
neighbor.py ... ok
niggli.py ... ok
noncollinear.py ... ok
pourbaix.py ... skipped ok
properties.py ... ok
pull.py ... ok
qmmm.py ... ok
rattle.py ... ok
repeat_FixAtoms.py ... ok
replay.py ... ok
root_test.py ... ok
rotate.py ... ok
rotate_euler.py ... ok
scaled_positions.py ... ok
scientificpython_bug.py ... skipped (no Scientific module) ok
set_get_angle.py ... ok
set_momenta.py ... ok
singlepointcalc.py ... ok
stm.py ... ok
strain.py ... ok
strain_emt.py ... ok
stress.py ... ok
surface.py ... ok
thermochemistry.py ... ok
things.py ... ok
tip3p.py ... ok
unitcellfilter.py ... ok
vacancy.py ... ok
verlet.py ... ok
vib.py ... ok
vtk_data.py ... ERROR
vtk_pipeline.py ... skipped ok
abinit/abinit_Si.py ... skipped ok
abinit/abinit_cmdline.py ... ok
aims/H2O_aims.py ... skipped ok
aims/aims_cmdline.py ... skipped ok
calculator/al.py ... ok
calculator/bandgap.py ... ok
calculator/h2.py ... ok
calculator/kd2mp.py ... ok
calculator/traj.py ... ok
castep/castep_interface.py ... ok
cmr/ase_rw.py ... skipped ok
cmr/cmr_rw.py ... ERROR
cmr/reactions.py ... ok
cmr/reactions_run.py ... skipped ok
cmr/reactions_test.py ... ERROR
cmr/reactions_xsimple.py ... ERROR
cmr/rw.py ... skipped ok
dftb/test_simple.py ... skipped ok
dftb/test_tricky.py ... skipped ok
elk/Al_rmt.py ... skipped ok
elk/elk_cmdline.py ... skipped ok
exciting/exciting.py ... skipped (no lxml module) ok
fio/abinit.py ... ok
fio/cfg.py ... ok
fio/extxyz.py ... ok
fio/info.py ... ok
fio/magmom.py ... ok
fio/netcdf.py ... /Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/scipy/io/netcdf.py:297: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.)
), category=RuntimeWarning)
ok
fio/netcdftrajectory.py ... skipped ok
fio/nwchem.py ... skipped ok
fio/oi.py ... ok
fio/oldtraj.py ... ok
fio/res.py ... ok
fio/trajectory.py ... ok
fio/v_sim.py ... ok
fleur/fleur_cmdline.py ... skipped ok
ga/basic_example_create_database.py ... ok
ga/basic_example_main_run.py ... ok
ga/create_database.py ... ok
ga/cutandsplicepairing.py ... ok
ga/database_logic.py ... ok
ga/element_operators.py ... ok
ga/mutations.py ... ok
ga/particle_comparators.py ... ok
ga/particle_operators.py ... ok
ga/standardcomparator.py ... ok
gaussian/gaussian_cmdline.py ... skipped ok
gaussian/h2of.py ... skipped ok
gaussian/water.py ... skipped ok
gromacs/test_gromacs.py ... skipped ok
jacapo/jacapo.py ... skipped (no Scientific module) ok
mopac/mopac_cmdline.py ... ERROR
nwchem/nwchem_broken_symmetry.py ... ok
nwchem/nwchem_cmdline.py ... skipped ok
nwchem/nwchem_h3o2m.py ... skipped ok
nwchem/nwchem_spin_symmetry.py ... ok
nwchem/nwchem_strong_levelshift.py ... ok
octopus/restart-octopus.py ... skipped ok
octopus/test-octopus.py ... skipped ok
tasks/analyse.py ... ERROR
tasks/dcdft.py ... ERROR
tasks/htb.py ... ERROR
tasks/optandfit.py ... ERROR
turbomole/turbomole_H2.py ... skipped ok
turbomole/turbomole_h3o2m.py ... skipped ok
vasp/vasp_Al_volrelax.py ... skipped ok
vasp/vasp_co.py ... skipped ok
COCu111.py ... ok
======================================================================
ERROR: aep1.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 52, in testfile
exec(compile(fd.read(), self.filename, 'exec'),
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/aep1.py", line 32
print m1
^
SyntaxError: invalid syntax
======================================================================
ERROR: al.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 52, in testfile
exec(compile(fd.read(), self.filename, 'exec'),
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/al.py", line 23
print calc.parameters, calc.results, calc.atoms
^
SyntaxError: invalid syntax
======================================================================
ERROR: vtk_data.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 52, in testfile
exec(compile(fd.read(), self.filename, 'exec'),
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/vtk_data.py", line 79
if self.verbose>1: print gc.get_objects()
^
SyntaxError: invalid syntax
======================================================================
ERROR: cmr/cmr_rw.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 53, in testfile
{'display': self.display})
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/cmr/cmr_rw.py", line 7, in <module>
import cmr
ImportError: No module named cmr
======================================================================
ERROR: cmr/reactions_test.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 52, in testfile
exec(compile(fd.read(), self.filename, 'exec'),
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/cmr/reactions_test.py", line 73
print 'reaction_id, calc, ref, calc - ref'
^
SyntaxError: invalid syntax
======================================================================
ERROR: cmr/reactions_xsimple.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 52, in testfile
exec(compile(fd.read(), self.filename, 'exec'),
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/cmr/reactions_xsimple.py", line 61
print "%s is missing"%formula
^
SyntaxError: invalid syntax
======================================================================
ERROR: mopac/mopac_cmdline.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 52, in testfile
exec(compile(fd.read(), self.filename, 'exec'),
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/mopac/mopac_cmdline.py", line 13
print ae
^
SyntaxError: invalid syntax
======================================================================
ERROR: tasks/analyse.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 52, in testfile
exec(compile(fd.read(), self.filename, 'exec'),
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/tasks/analyse.py", line 391
print 'skipped plotting empty data', r
^
SyntaxError: invalid syntax
======================================================================
ERROR: tasks/dcdft.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 53, in testfile
{'display': self.display})
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/tasks/dcdft.py", line 39, in <module>
from ase.tasks.bulk import BulkTask
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/tasks/bulk.py", line 8, in <module>
from ase.tasks.task import OptimizeTask
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/tasks/task.py", line 15, in <module>
from ase.utils import Lock, devnull, prnt
ImportError: cannot import name prnt
======================================================================
ERROR: tasks/htb.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 53, in testfile
{'display': self.display})
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/tasks/htb.py", line 35, in <module>
from ase.tasks.bulk import BulkTask
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/tasks/bulk.py", line 8, in <module>
from ase.tasks.task import OptimizeTask
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/tasks/task.py", line 15, in <module>
from ase.utils import Lock, devnull, prnt
ImportError: cannot import name prnt
======================================================================
ERROR: tasks/optandfit.py
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/__init__.py", line 53, in testfile
{'display': self.display})
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/test/tasks/optandfit.py", line 2, in <module>
from ase.tasks.main import run
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/tasks/main.py", line 7, in <module>
from ase.tasks.task import Task
File "/Users/mah/anaconda/envs/aseNew/lib/python2.7/site-packages/ase/tasks/task.py", line 15, in <module>
from ase.utils import Lock, devnull, prnt
ImportError: cannot import name prnt
----------------------------------------------------------------------
Ran 155 tests in 51.228s
FAILED (errors=11)
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