[ase-users] testing ase
Ask Hjorth Larsen
asklarsen at gmail.com
Thu Sep 13 16:03:41 CEST 2018
Dear José Carlos, (please respond to list; re-added list)
Am Do., 13. Sep. 2018 um 13:27 Uhr schrieb José Carlos Conesa
<jcconesa at icp.csic.es>:
>
> Hi Ask,
>
> I managed so that the administrators of my computer center installed
> newer versions of numpy, scipy and (I think) matplotlib. The I tried
> installing ase again (with setup.py build and setup.py install --user),
> it seemed to run well. then I tried again ase test and got the
> following output:
>
> ........................
>
> platform Linux-3.10.0-514.el7.x86_64-x86_64-with-redhat-7.3-Maipo
> python-2.7.5 /usr/bin/python
> ase-3.16.2 /home/icp/jcconesa/ase/ase/
> numpy-1.15.1 /home/icp/jcconesa/.local/lib/python2.7/site-packages/numpy/
> scipy-1.1.0 /home/icp/jcconesa/.local/lib/python2.7/site-packages/scipy/
> test-dir /tmp/ase-test-lKyXqr
>
> ..............E............s........................ss........E....s.......s................s....................s.ssss.....s......sssssssssssss......ss....ssssss..ss..s........ss...............s............ssssssss..ssssssss.sss..sssssssssssssss
> ======================================================================
> ERROR: bandstructure.py
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/home/icp/jcconesa/ase/ase/test/__init__.py", line 50, in testfile
> exec(compile(fd.read(), self.filename, 'exec'), {})
> File "/home/icp/jcconesa/ase/ase/test/bandstructure.py", line 1, in
> <module>
> import matplotlib
> File
> "/home/icp/jcconesa/.local/lib/python2.7/site-packages/matplotlib/__init__.py",
> line 130, in <module>
> from matplotlib.rcsetup import defaultParams, validate_backend, cycler
> File
> "/home/icp/jcconesa/.local/lib/python2.7/site-packages/matplotlib/rcsetup.py",
> line 29, in <module>
> from matplotlib.fontconfig_pattern import parse_fontconfig_pattern
> File
> "/home/icp/jcconesa/.local/lib/python2.7/site-packages/matplotlib/fontconfig_pattern.py",
> line 28, in <module>
> from backports.functools_lru_cache import lru_cache
> ImportError: No module named functools_lru_cache
Not sure how this can happen, but it looks like a matplotlib issue.
https://github.com/matplotlib/matplotlib/issues/9344
The stack trace indicates that the files are located in your ~/.local
directory, which means that it probably is not the same as the
administrators installed. Maybe remove the pip version to get the one
installed by the administrators. Also related: https://xkcd.com/1987/
>
> ======================================================================
> ERROR: matplotlib_plot.py
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/home/icp/jcconesa/ase/ase/test/__init__.py", line 50, in testfile
> exec(compile(fd.read(), self.filename, 'exec'), {})
> File "/home/icp/jcconesa/ase/ase/test/matplotlib_plot.py", line 1, in
> <module>
> import matplotlib.pyplot as plt
> File
> "/home/icp/jcconesa/.local/lib/python2.7/site-packages/matplotlib/__init__.py",
> line 126, in <module>
> from . import cbook
> ImportError: cannot import name cbook
This is probably caused by the same issue.
Both failures relate to matplotlib, so only plotting is broken.
Best regards
Ask
>
> ----------------------------------------------------------------------
> Ran 246 tests in 436.173s
>
> FAILED (errors=2, skipped=73)
>
> ....................................
>
> It seems thus that some error still remains. Some suggestions on how to
> get everything finally clean?
>
> All the best,
>
> José Carlos
> El 18/08/2018 a las 0:28, Ask Hjorth Larsen escribió:
> > Hi,
> >
> > Den fre. 17. aug. 2018 kl. 16.36 skrev José C. Conesa <jcconesa at icp.csic.es>:
> >> Hi,
> >>
> >> Good to know that the problem has been identified. Which minimum numpy version is required? I'll tell the administrator of the mainframe I'm using. And, are there minimum version requirements also for scipy and matplotlib?
> > I think it's numpy 1.9 whereas yours is 1.7.
> >
> > I am not sure about scipy requirements - we probably don't know it
> > exactly. Ubuntu 18.04 LTS presently has numpy 1.13 and scipy 0.19.
> > That, or newer, works. Matplotlib is 2.1.1.
> >
> > Best regards
> > Ask
> >
> >
> >> Thanks,
> >>
> >> JC Conesa
> >>
> >>
> >> El 17/08/2018 a las 22:41, Ask Hjorth Larsen escribió:
> >>
> >> Hi,
> >>
> >> Den fre. 17. aug. 2018 kl. 15.27 skrev José C. Conesa <jcconesa at icp.csic.es>:
> >>
> >> Hi,
> >>
> >> Attached is the result of command
> >>
> >> ase test Ag-Cu100.py CO2_Au111.py COCu111.py COCu111_2.py
> >>
> >> I hope this helps better.
> >>
> >> Thanks in advance,
> >>
> >> Right. The version of numpy is too old. (We should give a proper
> >> error message for that case.)
> >>
> >> Best regards
> >> Ask
> >>
> >> JC Conesa
> >>
> >>
> >> El 17/08/2018 a las 19:16, Ask Hjorth Larsen escribió:
> >>
> >> Hi,
> >>
> >>
> >>
> >> Den fre. 17. aug. 2018 kl. 02.29 skrev José C. Conesa <jcconesa at icp.csic.es>:
> >>
> >> Hi,
> >>
> >> In the attached file is the result of ase test -v
> >>
> >> Sorry, I should have asked for:
> >>
> >> ase test Ag-Cu100.py CO2_Au111.py COCu111.py COCu111_2.py
> >>
> >> or something similar. This should make sure that you get to see the
> >> stack traces for those errors instead of the test suite waiting
> >> forever and hence never printing them.
> >>
> >> Best regards
> >> Ask
> >>
> >>
> >> Hopefully this helps
> >>
> >>
> >> El 17/08/2018 a las 0:51, Ask Hjorth Larsen escribió:
> >>
> >> Hi,
> >>
> >> El jue., 16 ago. 2018 12:20, José C. Conesa via ase-users <ase-users at listserv.fysik.dtu.dk> escribió:
> >>
> >> Hi,
> >>
> >> I have just downloaded ase-3.6.12 and installed it in a Linux mainframe which already had installed python 2.7, scipy, numpy and matplotlib. I added the proper definitions to $PYTHONPATH and $PATH. When I type ase test I get the following result:
> >>
> >> platform Linux-3.10.0-514.el7.x86_64-x86_64-with-redhat-7.3-Maipo
> >> python-2.7.5 /usr/bin/python
> >> ase-3.16.2 /home/icp/jcconesa/ase/ase/
> >> numpy-1.7.1 /usr/lib64/python2.7/site-packages/numpy/
> >> scipy-0.12.1 /usr/lib64/python2.7/site-packages/scipy/
> >> test-dir /tmp/ase-test-4ge6yM
> >>
> >> EEEE...E...E...E........E..sE.E..EE....E.E.E.E.....Ess.E.E.E....E.Es.EE.E..s....EEE.E.E.....sE.E.............EE..s.ssss....Es......sssssssssssss.E.s..ss....ssssss..ss..s....E.E.ssEE....EEE.E
> >>
> >> and the command seems to remain stuck; it has been running for more than 25 min already. ls -l /tmp/ase-test-4ge6yM shows that all its content was generated in the first minute, no further change is revealed.
> >>
> >> Is there some failure?
> >>
> >> Yes, this is not supposed to happen. Please rerun with -v to get more info.
> >>
> >> Best regards
> >> Ask
> >>
> >>
> >>
> >> Thanks,
> >>
> >>
> >> José C. Conesa
> >> Instituto de Catálisis y Petroleoquímica, CSIC
> >> Marie Curie 2, Cantoblanco
> >> 28049 Madrid, Spain
> >> Tel. (+34)915854766
> >>
> >>
> >> Libre de virus. www.avast.com
> >> _______________________________________________
> >> ase-users mailing list
> >> ase-users at listserv.fysik.dtu.dk
> >> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> >>
> >> --
> >> José C. Conesa
> >> Instituto de Catálisis y Petroleoquímica, CSIC
> >> Marie Curie 2, Cantoblanco
> >> 28049 Madrid, Spain
> >> Tel. (+34)915854766
> >>
> >>
> >> --
> >> José C. Conesa
> >> Instituto de Catálisis y Petroleoquímica, CSIC
> >> Marie Curie 2, Cantoblanco
> >> 28049 Madrid, Spain
> >> Tel. (+34)915854766
> >>
> >>
> >> Libre de virus. www.avast.com
> >>
> >>
> >> --
> >> José C. Conesa
> >> Instituto de Catálisis y Petroleoquímica, CSIC
> >> Marie Curie 2, Cantoblanco
> >> 28049 Madrid, Spain
> >> Tel. (+34)915854766
> >>
> >>
> >> Libre de virus. www.avast.com
>
> --
> José C. Conesa
> Instituto de Catálisis y Petroleoquímica, CSIC
> Marie Curie 2, Madrid, Spain
> www.icp.csic.es
> Tel. (+34)915854766
>
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