Comments (6)
tovrstra
commented on July 3, 2024
Could this be the same issue as reported here: lucasb-eyer/pydensecrf#28. If yes, the solution would be to install libgcc in conda:
conda install libgccThere could be other reasons for this, so please let us know if it worked. Mixing up conda compilers with the ones from your Linux distribution is often a source of confusion.
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PeaWagon
commented on July 3, 2024
Okay I think that worked for the conda version. Thanks.
I'm still trying to get the github version to work though. When I try to import horton from the github repository that I forked, I get the following error:
(py27) jgarne01@oryx:~/ExtraDrive/githubcode/horton$ python
Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import horton
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "horton/__init__.py", line 28, in <module>
from horton.cext import *
ImportError: No module named cext
When I try to import horton anywhere else, it works. This version of horton is listed in my "conda list".
horton 2.1.0 <pip>
Here are the tests that I ran using nosetests:
======================================================================
ERROR: horton.part.test.test_proatomdb.test_compute_radii
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/part/test/test_proatomdb.py", line 128, in test_compute_radii
record = padb.get_record(6, 0)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/part/proatomdb.py", line 358, in get_record
return self._map[(number, charge)]
KeyError: (6, 0)
======================================================================
ERROR: horton.part.test.test_proatomdb.test_get_spline
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/part/test/test_proatomdb.py", line 172, in test_get_spline
spline = padb.get_spline(6)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/part/proatomdb.py", line 597, in get_spline
rho, deriv = self.get_rho(number, parameters, combine, do_deriv=True)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/part/proatomdb.py", line 547, in get_rho
record = self.get_record(number, charge)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/part/proatomdb.py", line 358, in get_record
return self._map[(number, charge)]
KeyError: (6, 0)
======================================================================
FAIL: horton.part.test.test_proatomdb.test_db_basics
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/part/test/test_proatomdb.py", line 32, in test_db_basics
assert padb.get_numbers() == [1, 8]
AssertionError
======================================================================
FAIL: horton.part.test.test_proatomdb.test_io_group
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/part/test/test_proatomdb.py", line 103, in test_io_group
assert padb1.size == 5
AssertionError
======================================================================
FAIL: horton.part.test.test_proatomdb.test_io_filename
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/part/test/test_proatomdb.py", line 116, in test_io_filename
assert keys == [(1, 0), (6, 0), (6, 1)]
AssertionError
======================================================================
FAIL: horton.scripts.test.test_atomdb.test_plot_atoms
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/scripts/test/test_atomdb.py", line 209, in test_plot_atoms
check_files(dn, fns)
File "/home/jgarne01/anaconda3/envs/py27/lib/python2.7/site-packages/horton/scripts/test/common.py", line 39, in check_files
assert os.path.isfile(os.path.join(dn, fn)), "Missing %s" % fn
AssertionError: Missing dens_001__h.png
----------------------------------------------------------------------
Ran 979 tests in 205.954s
FAILED (SKIP=1, errors=2, failures=4)
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tovrstra
commented on July 3, 2024
You need to take the step explained here, in case you work with the version from git:
http://theochem.github.io/horton/2.1.0/tech_dev_git.html#reference-atoms
Also, when you just get the version from git, the c extensions still have to be built, just like when you install from source. This is why you get the error ImportError: No module named cext. You either do a complete install of the git version (and uninstall the other version first) or you can do an in-place build with ./setup.py build_ext -i. Also keep in mind that the current latest version from git works with libxc-3.0.0.
In any case, I would strongly recommend to work only with one version of HORTON at a time on your system. Having two versions, like you do now, may give you a lot of confusion error messages.
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PeaWagon
commented on July 3, 2024
Okay, I have removed all of the versions of horton and just installed the github version. I can import horton from anywhere except the horton github directory (in that case, it gives the ImportError: No module named cext). What is the expected behaviour when importing from the horton directory? Should it work or do I have to something extra?
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PeaWagon
commented on July 3, 2024
Never mind my last comment. It seems that when I installed horton without the user argument it put my files in the correct anaconda environment directory. You can close this issue now if you'd like.
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tovrstra
commented on July 3, 2024
Both observations seem to be the normal behavior. (i) When you import a package in Python, it will first look for that package in the current directory, which in this case does not work because the cext.so file is not there. (ii) The --user option should indeed not be used when you want to install into conda or virtualenv.
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