[ase-users] Installation failed in Ubuntu Linux
Ask Hjorth Larsen
asklarsen at gmail.com
Tue Jan 5 15:35:46 CET 2016
Hello
(Re-added mailing list to recipients)
Oh, right, you did mention 14.04.... probably a manual installation is fine.
The problem seems to be in some cases that it certain files already exist.
Just make sure that the tests do not run twice in the same directory, e.g.,
by going to a new directory.
Best regards
Ask
2016-01-05 12:19 GMT+01:00 Santu Baidya <santubaidya2009 at gmail.com>:
> I am using Ubuntu 14.04 LTS version. Please tell me what should I use in
> this case.
>
> Thanking you,
>
> Santu Baidya
>
>
>
>
> On 5 January 2016 at 05:01, Ask Hjorth Larsen <asklarsen at gmail.com> wrote:
>
>> Hello
>>
>> This looks like it is the fault of the tests more than anything else.
>> Apparently it is trying to overwrite some files that were most likely (and
>> hopefully :)) produced during a previous run of the test suite.
>>
>> If you are using Ubuntu 15.10, you should be able to install python-ase
>> (ASE 3.9.1) from the standard repositories. With Ubuntu 15.04 as well,
>> except only version 3.8.1.
>>
>> A different and hopefully more well-behaved way to run the tests is to do
>> 'python setup.py test'.
>>
>> Does this help?
>>
>> Best regards
>> Ask
>>
>> 2015-12-29 10:28 GMT+01:00 Santu Baidya <santubaidya2009 at gmail.com>:
>>
>>> Dear ASE community,
>>>
>>>
>>> I am trying to install the ASE Version: 3.9.1.4567 in Ubuntu 14.04
>>> LTS Linux . I have I followed the steps from installation guide from
>>> website https://wiki.fysik.dtu.dk/ase/download.html.
>>>
>>> After installation when I tried to test installation using the command
>>> ...
>>> "python -c "from ase.test import test; test(verbosity=2, display=True)"
>>> 2>&1 | tee testase.log"
>>> it failed with error..............
>>>
>>> python 2.7.6 GCC 4.8.2 64bit ELF on Linux x86_64 Ubuntu 14.04 trusty
>>> Ag-Cu100.py (ScriptTestCase) ... ok
>>> CO2_Au111.py (ScriptTestCase) ... ok
>>> COCu111_2.py (ScriptTestCase) ... ok
>>> aff.py (ScriptTestCase) ... ok
>>> ag.py (ScriptTestCase) ... ok
>>> atom.py (ScriptTestCase) ... ok
>>> atoms_distance.py (ScriptTestCase) ... ok
>>> atoms_info_copy.py (ScriptTestCase) ... ok
>>> bader.py (ScriptTestCase) ... ok
>>> bandgap.py (ScriptTestCase) ... ok
>>> basin.py (ScriptTestCase) ... ok
>>> build.py (ScriptTestCase) ... ok
>>> bulk.py (ScriptTestCase) ... ok
>>> center.py (ScriptTestCase) ... ok
>>> com.py (ScriptTestCase) ... ok
>>> constr_setpos.py (ScriptTestCase) ... ok
>>> coverage.py (ScriptTestCase) ... ok
>>> crystal.py (ScriptTestCase) ... ok
>>> db.py (ScriptTestCase) ... Running: H
>>> Running: H2O
>>> Running: O2
>>> Running: H2
>>> LBFGS: 0 18:22:05 1.158864 4.4619
>>> LBFGS: 1 18:22:05 1.129374 2.9285
>>> LBFGS: 2 18:22:05 1.072359 0.5614
>>> LBFGS: 3 18:22:05 1.070596 0.0991
>>> LBFGS: 4 18:22:05 1.070541 0.0026
>>> Running: O2
>>> LBFGS: 0 18:22:05 0.922681 3.7034
>>> LBFGS: 1 18:22:05 0.691988 1.9589
>>> LBFGS: 2 18:22:05 0.628304 0.5011
>>> LBFGS: 3 18:22:05 0.624816 0.0669
>>> LBFGS: 4 18:22:05 0.624750 0.0019
>>> Running: Cu
>>> Deleted 1 row
>>> Added 12 key-value pairs (6 pairs updated)
>>> Removed 0 key-value pairs
>>> Added 0 key-value pairs (0 pairs updated)
>>> Removed 6 key-value pairs
>>> FAIL
>>> db2.py (ScriptTestCase) ... ok
>>> dependency_backend_gdk.py (ScriptTestCase) ... ok
>>> dependency_backend_gtkagg.py (ScriptTestCase) ... ok
>>> dependency_gtk.py (ScriptTestCase) ... ok
>>> dependency_matplotlib.py (ScriptTestCase) ... ok
>>> dihedralconstraint.py (ScriptTestCase) ... ok
>>> dimer.py (ScriptTestCase) ... ok
>>> dimer_method.py (ScriptTestCase) ... ok
>>> distance.py (ScriptTestCase) ... ok
>>> distmom.py (ScriptTestCase) ... ok
>>> eam_test.py (ScriptTestCase) ... ok
>>> emt.py (ScriptTestCase) ... ok
>>> emt1.py (ScriptTestCase) ... ok
>>> emt2.py (ScriptTestCase) ... ok
>>> emt_h3o2m.py (ScriptTestCase) ... ok
>>> eos.py (ScriptTestCase) ... ok
>>> eoswoase.py (ScriptTestCase) ... ok
>>> example.py (ScriptTestCase) ... ok
>>> fcc111_root.py (ScriptTestCase) ... ok
>>> fix_bond_length_mic.py (ScriptTestCase) ... ok
>>> geometry.py (ScriptTestCase) ... ok
>>> h2.py (ScriptTestCase) ... ok
>>> hcp.py (ScriptTestCase) ... ok
>>> idpp.py (ScriptTestCase) ... ok
>>> maxwellboltzmann.py (ScriptTestCase) ... ok
>>> md.py (ScriptTestCase) ... ok
>>> mic.py (ScriptTestCase) ... ok
>>> minimahop.py (ScriptTestCase) ... ok
>>> n2.py (ScriptTestCase) ... ok
>>> neb.py (ScriptTestCase) ... ok
>>> neighbor.py (ScriptTestCase) ... ok
>>> niggli.py (ScriptTestCase) ... ok
>>> noncollinear.py (ScriptTestCase) ... ok
>>> pourbaix.py (ScriptTestCase) ... skipped ok
>>> properties.py (ScriptTestCase) ... ok
>>> pull.py (ScriptTestCase) ... ok
>>> repeat_FixAtoms.py (ScriptTestCase) ... ok
>>> replay.py (ScriptTestCase) ... ok
>>> rotate.py (ScriptTestCase) ... ok
>>> rotate_euler.py (ScriptTestCase) ... ok
>>> scaled_positions.py (ScriptTestCase) ... ok
>>> scientificpython_bug.py (ScriptTestCase) ... (skipped) ok
>>> set_get_angle.py (ScriptTestCase) ... ok
>>> set_momenta.py (ScriptTestCase) ... ok
>>> singlepointcalc.py (ScriptTestCase) ... ok
>>> stm.py (ScriptTestCase) ... ok
>>> strain.py (ScriptTestCase) ... ok
>>> strain_emt.py (ScriptTestCase) ... ok
>>> stress.py (ScriptTestCase) ... ok
>>> surface.py (ScriptTestCase) ... ok
>>> things.py (ScriptTestCase) ... ok
>>> unitcellfilter.py (ScriptTestCase) ... ok
>>> vacancy.py (ScriptTestCase) ... ok
>>> verlet.py (ScriptTestCase) ... ok
>>> vib.py (ScriptTestCase) ... ok
>>> vtk_pipeline.py (ScriptTestCase) ... skipped ok
>>> abinit/abinit_Si.py (ScriptTestCase) ... skipped ok
>>> abinit/abinit_cmdline.py (ScriptTestCase) ... ok
>>> aims/H2O_aims.py (ScriptTestCase) ... skipped ok
>>> aims/aims_cmdline.py (ScriptTestCase) ... skipped ok
>>> calculator/al.py (ScriptTestCase) ... ok
>>> calculator/bandgap.py (ScriptTestCase) ... ok
>>> calculator/h2.py (ScriptTestCase) ... ok
>>> calculator/kd2mp.py (ScriptTestCase) ... ok
>>> calculator/traj.py (ScriptTestCase) ... ERROR
>>> castep/castep_interface.py (ScriptTestCase) ... skipped ok
>>> cmr/ase_rw.py (ScriptTestCase) ... skipped ok
>>> cmr/cmr_rw.py (ScriptTestCase) ... (skipped) ok
>>> cmr/reactions.py (ScriptTestCase) ... ok
>>> cmr/reactions_run.py (ScriptTestCase) ... skipped ok
>>> cmr/reactions_test.py (ScriptTestCase) ... skipped ok
>>> cmr/reactions_xsimple.py (ScriptTestCase) ... skipped ok
>>> cmr/rw.py (ScriptTestCase) ... skipped ok
>>> dftb/test_simple.py (ScriptTestCase) ... skipped ok
>>> dftb/test_tricky.py (ScriptTestCase) ... skipped ok
>>> elk/Al_rmt.py (ScriptTestCase) ... skipped ok
>>> elk/elk_cmdline.py (ScriptTestCase) ... skipped ok
>>> exciting/exciting.py (ScriptTestCase) ... skipped ok
>>> fio/abinit.py (ScriptTestCase) ... ok
>>> fio/cfg.py (ScriptTestCase) ... ok
>>> fio/extxyz.py (ScriptTestCase) ... ok
>>> fio/info.py (ScriptTestCase) ... ok
>>> fio/magmom.py (ScriptTestCase) ... ok
>>> fio/netcdf.py (ScriptTestCase) ... ok
>>> fio/netcdftrajectory.py (ScriptTestCase) ... skipped ok
>>> fio/nwchem.py (ScriptTestCase) ... skipped ok
>>> fio/oi.py (ScriptTestCase) ... ERROR
>>> fio/oldtraj.py (ScriptTestCase) ... ok
>>> fio/res.py (ScriptTestCase) ... ok
>>> fio/trajectory.py (ScriptTestCase) ... ok
>>> fio/v_sim.py (ScriptTestCase) ... skipped ok
>>> fleur/fleur_cmdline.py (ScriptTestCase) ... skipped ok
>>> ga/basic_example_create_database.py (ScriptTestCase) ... ok
>>> ga/basic_example_main_run.py (ScriptTestCase) ... ok
>>> ga/create_database.py (ScriptTestCase) ... ok
>>> ga/cutandsplicepairing.py (ScriptTestCase) ... ok
>>> ga/database_logic.py (ScriptTestCase) ... ok
>>> ga/element_operators.py (ScriptTestCase) ... ok
>>> ga/mutations.py (ScriptTestCase) ... ok
>>> ga/particle_comparators.py (ScriptTestCase) ... ok
>>> ga/particle_operators.py (ScriptTestCase) ... ok
>>> ga/standardcomparator.py (ScriptTestCase) ... ok
>>> gaussian/gaussian_cmdline.py (ScriptTestCase) ... skipped ok
>>> gaussian/h2of.py (ScriptTestCase) ... skipped ok
>>> gaussian/water.py (ScriptTestCase) ... skipped ok
>>> gromacs/test_gromacs.py (ScriptTestCase) ... skipped ok
>>> jacapo/jacapo.py (ScriptTestCase) ... (skipped) ok
>>> mopac/mopac_cmdline.py (ScriptTestCase) ... skipped ok
>>> nwchem/nwchem_broken_symmetry.py (ScriptTestCase) ... ok
>>> nwchem/nwchem_cmdline.py (ScriptTestCase) ... skipped ok
>>> nwchem/nwchem_h3o2m.py (ScriptTestCase) ... skipped ok
>>> nwchem/nwchem_spin_symmetry.py (ScriptTestCase) ... ok
>>> nwchem/nwchem_strong_levelshift.py (ScriptTestCase) ... ok
>>> tasks/analyse.py (ScriptTestCase) ... ok
>>> tasks/dcdft.py (ScriptTestCase) ... ok
>>> tasks/gbrv.py (ScriptTestCase) ... ok
>>> tasks/htb.py (ScriptTestCase) ... ok
>>> tasks/mmbjmp.py (ScriptTestCase) ... ok
>>> turbomole/turbomole_H2.py (ScriptTestCase) ... skipped ok
>>> turbomole/turbomole_h3o2m.py (ScriptTestCase) ... skipped ok
>>> vasp/vasp_Al_volrelax.py (ScriptTestCase) ... skipped ok
>>> vasp/vasp_co.py (ScriptTestCase) ... skipped ok
>>> COCu111.py (ScriptTestCase) ...
>>> /usr/lib/pymodules/python2.7/matplotlib/backends/backend_gtk.py:250:
>>> Warning: Source ID 31 was not found when attempting to remove it
>>> gobject.source_remove(self._idle_event_id)
>>> ok
>>>
>>> ======================================================================
>>> ERROR: calculator/traj.py (ScriptTestCase)
>>> ----------------------------------------------------------------------
>>> Traceback (most recent call last):
>>> File "/home/santuphys/ase/ase/test/__init__.py", line 51, in testfile
>>> {'display': self.display})
>>> File "/home/santuphys/ase/ase/test/calculator/traj.py", line 35, in
>>> <module>
>>> os.mkdir(name + '-test')
>>> OSError: [Errno 17] File exists: 'emt-test'
>>>
>>> ======================================================================
>>> ERROR: fio/oi.py (ScriptTestCase)
>>> ----------------------------------------------------------------------
>>> Traceback (most recent call last):
>>> File "/home/santuphys/ase/ase/test/__init__.py", line 51, in testfile
>>> {'display': self.display})
>>> File "/home/santuphys/ase/ase/test/fio/oi.py", line 86, in <module>
>>> assert np.all(np.abs(a1.get_positions() -
>>> AttributeError: 'list' object has no attribute 'get_positions'
>>>
>>> ======================================================================
>>> FAIL: db.py (ScriptTestCase)
>>> ----------------------------------------------------------------------
>>> Traceback (most recent call last):
>>> File "/home/santuphys/ase/ase/test/__init__.py", line 51, in testfile
>>> {'display': self.display})
>>> File "/home/santuphys/ase/ase/test/db.py", line 23, in <module>
>>> assert len(list(con.select())) == 5
>>> AssertionError
>>>
>>> ----------------------------------------------------------------------
>>> Ran 142 tests in 97.821s
>>>
>>> FAILED (failures=1, errors=2)
>>>
>>>
>>> The testase.log is attached herewith this mail. In the website of ASE it
>>> is written that is tests fales to send mail to this email id.
>>>
>>> Please help me to install it successfully.
>>>
>>>
>>> Thanking you,
>>>
>>> Santu Baidya
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> ase-users mailing list
>>> ase-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>>
>>
>>
>
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