[gpaw-users] gpaw-users Digest, Vol 77, Issue 29
Toma Susi
toma.susi at univie.ac.at
Thu Jun 30 12:11:12 CEST 2016
> On 30 Jun 2016, at 12:00, gpaw-users-request at listserv.fysik.dtu.dk wrote:
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> Today's Topics:
>
> 1. Re: Several tests fail on gpaw 0.11 installed using pip on
> Mac OSX El capitan (Rasmus Karlsson) (Jens J?rgen Mortensen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 30 Jun 2016 10:43:13 +0200
> From: Jens J?rgen Mortensen <jensj at fysik.dtu.dk>
> To: Rasmus Karlsson <rasmusk at kth.se>, Toma Susi
> <toma.susi at univie.ac.at>
> Cc: gpaw-users at listserv.fysik.dtu.dk
> Subject: Re: [gpaw-users] Several tests fail on gpaw 0.11 installed
> using pip on Mac OSX El capitan (Rasmus Karlsson)
> Message-ID: <5774DBA1.9010708 at fysik.dtu.dk>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> On 06/29/2016 06:48 PM, Rasmus Karlsson via gpaw-users wrote:
>>
>> Toma Susi via gpaw-users writes:
>>
>>> Hi Rasmus,
>>>
>>> and thanks for testing this out! I'm ashamed to admit I didn't check the
>>> tests since I figured my system on this separate user account isn't
>>> representative of a clean install anyways.
>>>
>>> Assertion errors with small excesses over the tolerances are usually not
>>> a serious issue, but I can confirm that I reproduce the exact same
>>> errors.
>>>
>>> In addition, I get several failed tests with a locale error:
>>>
>>> Traceback (most recent call last):
>>> File "/usr/local/lib/python2.7/site-packages/gpaw/test/__init__.py",
>>> line 584, in run_one
>>> exec(compile(open(filename).read(), filename, 'exec'), loc)
>>> File "/usr/local/lib/python2.7/site-packages/gpaw/test/ut_tddft.py",
>>> line 7, in <module>
>>> import matplotlib as mpl
>>> File "/usr/local/lib/python2.7/site-packages/matplotlib/__init__.py",
>>> line 1131, in <module>
>>> rcParams = rc_params()
>>> File "/usr/local/lib/python2.7/site-packages/matplotlib/__init__.py",
>>> line 975, in rc_params
>>> return rc_params_from_file(fname, fail_on_error)
>>> File "/usr/local/lib/python2.7/site-packages/matplotlib/__init__.py",
>>> line 1100, in rc_params_from_file
>>> config_from_file = _rc_params_in_file(fname, fail_on_error)
>>> File "/usr/local/lib/python2.7/site-packages/matplotlib/__init__.py",
>>> line 1018, in _rc_params_in_file
>>> with _open_file_or_url(fname) as fd:
>>> File
>>> "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/contextlib.py",
>>> line 17, in __enter__
>>> return self.gen.next()
>>> File "/usr/local/lib/python2.7/site-packages/matplotlib/__init__.py",
>>> line 1000, in _open_file_or_url
>>> encoding = locale.getdefaultlocale()[1]
>>> File
>>> "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
>>> line 543, in getdefaultlocale
>>> return _parse_localename(localename)
>>> File
>>> "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/locale.py",
>>> line 475, in _parse_localename
>>> raise ValueError, 'unknown locale: %s' % localename
>>> ValueError: unknown locale: UTF-8
>>>
>>> Is there an easy fix for this?
>
> This seems to be a matplotlib problem. Are you able to use matplotlib
> at all?
>
> Jens J?rgen
Ah, sorry – this was due to incorrect (default) terminal settings on my test user account. Mac OSX users need to disable
"Set locale environment variables on startup"
in the Terminal -> Preferences -> Profiles -> Advanced tab.
It might be a good idea to add a mention of this to the instructions.
-Toma
P.S. I can't really help with changing the tolerances and Git, sorry..
>
>>>
>>> -----------
>>>
>>> Best,
>>> Toma
>>>
>>> P.S. I actually had another remaining issue: some tests were failing due
>>> to "ImportError: No module named _ufuncs" error. This was fixed by
>>> reinstalling Scipy using the "Superpack" installer created by Chris
>>> Fonnesbeck (http://stronginference.com/ScipySuperpack/).
>>>
>>> This might be good way to streamline the GPAW installation further,
>>> since the Superpack also installs Numpy and Matplotlib, and even
>>> Homebrew, Git and Xcode Tools if those are not installed yet.
>>>
>>>
>>>
>>> Am 29.06.2016 12:00, schrieb gpaw-users-request at listserv.fysik.dtu.dk:
>>>> Send gpaw-users mailing list submissions to
>>>> gpaw-users at listserv.fysik.dtu.dk
>>>>
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>>>> or, via email, send a message with subject or body 'help' to
>>>> gpaw-users-request at listserv.fysik.dtu.dk
>>>>
>>>> You can reach the person managing the list at
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>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of gpaw-users digest..."
>>>>
>>>>
>>>> Today's Topics:
>>>>
>>>> 1. Several tests fail on gpaw 0.11 installed using pip on Mac
>>>> OSX El capitan (Rasmus Karlsson)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Tue, 28 Jun 2016 15:29:37 -0700
>>>> From: Rasmus Karlsson <rasmusk at kth.se>
>>>> To: gpaw-users at listserv.fysik.dtu.dk
>>>> Subject: [gpaw-users] Several tests fail on gpaw 0.11 installed using
>>>> pip on Mac OSX El capitan
>>>> Message-ID: <m2vb0t54mm.fsf at kth.se>
>>>> Content-Type: text/plain
>>>>
>>>> Hi,
>>>>
>>>> On my freshly installed GPAW 0.11, installed using pip install --user
>>>> gpaw, several tests fail. The tests are run using 'gpaw test'.
>>>>
>>>> The following tests fail:
>>>> rasmusk at rasmus-macbook:/tmp/test2$ gpaw test -j 3
>>>> python-2.7.11 /usr/local/opt/python/bin/python2.7
>>>> gpaw-1.1.0
>>>> /Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/
>>>> ase-3.11.0 /usr/local/lib/python2.7/site-packages/ase/
>>>> numpy-1.11.1 /usr/local/lib/python2.7/site-packages/numpy/
>>>> scipy-0.17.1 /usr/local/lib/python2.7/site-packages/scipy/
>>>> _gpaw
>>>> /Users/rasmusk/Library/Python/2.7/lib/python/site-packages/_gpaw.so
>>>> parallel /Users/rasmusk/Library/Python/2.7/bin/gpaw-python
>>>> FFTW no
>>>> scalapack no
>>>> libvdwxc no
>>>> PAW-datasets 1: /Users/rasmusk/gpaw-setups/gpaw-setups-0.9.11271
>>>> 2: /usr/local/share/gpaw-setups
>>>> 3: /usr/share/gpaw-setups
>>>> Running tests in
>>>> /var/folders/23/3tv2l9s565v7pf_vzpczl6c80000gn/T/gpaw-test-bPH2Bb
>>>> Jobs: 3, Cores: 1, debug-mode: False
>>>> =============================================================================
>>>>
>>>> solvation/vacuum.py 5.470 FAILED!
>>>> #############################################################################
>>>> Traceback (most recent call last):
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 577, in run_one
>>>> exec(compile(open(filename).read(), filename, 'exec'), loc)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/solvation/vacuum.py",
>>>> line 62, in <module>
>>>> equal(Etest, Eref, dE)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 28, in equal
>>>> raise AssertionError(msg)
>>>> AssertionError: -11.9838020445 != -11.9837925246 (error:
>>>> |-9.51991932929e-06| > 1e-09)
>>>> #############################################################################
>>>>
>>>> inducedfield_lrtddft.py 7.839 FAILED!
>>>> #############################################################################
>>>> Traceback (most recent call last):
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 577, in run_one
>>>> exec(compile(open(filename).read(), filename, 'exec'), loc)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/inducedfield_lrtddft.py",
>>>> line 48, in <module>
>>>> equal(val1, 3175.76308, tol)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 28, in equal
>>>> raise AssertionError(msg)
>>>> AssertionError: 3175.76177698 != 3175.76308 (error:
>>>> |-0.00130302261596| > 0.0001)
>>>> #############################################################################
>>>>
>>>> fdtd/ed_wrapper.py 23.614 FAILED!
>>>> #############################################################################
>>>> Traceback (most recent call last):
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 577, in run_one
>>>> exec(compile(open(filename).read(), filename, 'exec'), loc)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/fdtd/ed_wrapper.py",
>>>> line 43, in <module>
>>>>
>>>> equal(qsfdtd.td_calc.hamiltonian.poisson.get_quantum_dipole_moment(),
>>>> ref_qm_dipole_moment, tol)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 28, in equal
>>>> raise AssertionError(msg)
>>>> AssertionError: [ 2.87661347e-10 1.99335501e-10 -9.35618521e-02]
>>>> != [-2.63340461e-11, 2.61812794e-12, 0.521368171] (error: |[
>>>> 3.13995393e-10 1.96717373e-10 -6.14930023e-01]| > 0.0001)
>>>> #############################################################################
>>>>
>>>> fdtd/ed.py 23.509 FAILED!
>>>> #############################################################################
>>>> Traceback (most recent call last):
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 577, in run_one
>>>> exec(compile(open(filename).read(), filename, 'exec'), loc)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/fdtd/ed.py",
>>>> line 83, in <module>
>>>> equal(td_calc2.hamiltonian.poisson.get_quantum_dipole_moment(),
>>>> ref_qm_dipole_moment, tol)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 28, in equal
>>>> raise AssertionError(msg)
>>>> AssertionError: [ 1.16182518e-09 -6.61938227e-11 -9.35619379e-02]
>>>> != [-2.63340461e-11, 2.61812794e-12, 0.521368171] (error: |[
>>>> 1.18815922e-09 -6.88119506e-11 -6.14930109e-01]| > 0.0001)
>>>> #############################################################################
>>>>
>>>> complex.py 6.133 FAILED!
>>>> #############################################################################
>>>> Traceback (most recent call last):
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 577, in run_one
>>>> exec(compile(open(filename).read(), filename, 'exec'), loc)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/complex.py",
>>>> line 23, in <module>
>>>> equal(Eini, Eini0, 1E-8)
>>>> File
>>>> "/Users/rasmusk/Library/Python/2.7/lib/python/site-packages/gpaw/test/__init__.py",
>>>> line 28, in equal
>>>> raise AssertionError(msg)
>>>> AssertionError: -17.8037677573 != -17.8037610364 (error:
>>>> |-6.72086014575e-06| > 1e-08)
>>>> #############################################################################
>>>>
>>>> Does anyone have any suggestions for what might fix these errors?
>>>>
>>>> Thanks,
>>>> Rasmus
>>>> --
>>>> Rasmus Karlsson, PhD
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> gpaw-users mailing list
>>>> gpaw-users at listserv.fysik.dtu.dk
>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>>
>>>> End of gpaw-users Digest, Vol 77, Issue 27
>>>> ******************************************
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>>
>
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