Hi Pablo,
Do you get both "Module vsc was already imported" and "Module easybuild
was already imported" warnings on this system?
K.
On 05/02/16 11:05, Pablo Escobar Lopez wrote:
in case it helps, I have noticed that I only get these warnings in the
machine were i have python-keyring installed.
this is my output for the command that Kenneth asks (identical is the
machine which triggers the warning and in the machine which doesn't
trigger the warning)
[escobar@login18 easybuild-easyconfigs]$ python -c 'import sys;print
sys.version;import vsc;print vsc.__path__;import easybuild;print
easybuild.__path__'
2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]
['/scicore/soft/apps/EasyBuild/2.6.0/lib/python2.6/site-packages/vsc_base-2.2.4-py2.6.egg/vsc']
['/scicore/soft/apps/EasyBuild/2.6.0/lib/python2.6/site-packages/easybuild_framework-2.6.0-py2.6.egg/easybuild',
'/scicore/soft/apps/EasyBuild/2.6.0/lib/python2.6/site-packages/easybuild_easyblocks-2.6.0-py2.6.egg/easybuild']
2016-02-05 10:06 GMT+01:00 Kenneth Hoste <[email protected]
<mailto:[email protected]>>:
Hi Judith,
We're looking into a solution for these warnings, both in vsc-base
and EasyBuild, see also
https://github.com/hpcugent/easybuild-framework/issues/1588
Can you provide us the output of the following command?
python -c 'import sys;print sys.version;import vsc;print
vsc.__path__;import easybuild;print easybuild.__path__'
regards,
Kenneth
On 03/02/16 19:13, Kenneth Hoste wrote:
Hi Judith,
On 28/01/16 22:37, Gardiner, Judith wrote:
[ruby01]$ eb --version
/usr/local/easybuild/2.6.0/software/EasyBuild/2.6.0/lib/python2.6/site-packages/vsc_base-2.4.16-py2.6.egg/vsc/__init__.py:29:
UserWarning: Module vsc was already imported from
/usr/local/easybuild/2.6.0/software/EasyBuild/2.6.0/lib/python2.6/site-packages/vsc_base-2.4.16-py2.6.egg/vsc/__init__.pyc,
but
/usr/local/easybuild/2.6.0/software/EasyBuild/2.6.0/lib/python2.6/site-packages/vsc_install-0.9.12-py2.6.egg
is being added to sys.path
import pkg_resources
/usr/local/easybuild/2.6.0/software/EasyBuild/2.6.0/lib/python2.6/site-packages/vsc_base-2.4.16-py2.6.egg/vsc/__init__.py:29:
UserWarning: Module easybuild was already imported from
/usr/local/easybuild/2.6.0/software/EasyBuild/2.6.0/lib/python2.6/site-packages/easybuild_framework-2.6.0-py2.6.egg/easybuild/__init__.pyc,
but
/usr/local/easybuild/2.6.0/software/EasyBuild/2.6.0/lib/python2.6/site-packages/easybuild_easyblocks-2.6.0-py2.6.egg
is being added to sys.path
import pkg_resources
This is EasyBuild 2.6.0 (framework: 2.6.0, easyblocks: 2.6.0) on
host ruby01.osc.edu <http://ruby01.osc.edu>.
First of all, these warnings are harmless in the sense that
everything will work even though they are being spit out.
I agree they are ugly though, and we should try and get rid of them.
The problem is that vsc-base was split up recently, into what
vsc-base is now and vsc-install, which provides support for
installing/testing vsc-* packages.
This implies that the 'vsc' namespace is spread across two
different directories now, and that "import vsc" in Python will
result in reading vsc/__init__.py from two different places.
Python (or setuptools?) thinks this is weird, and throws the
warnings.
Same applies to the 'easybuild' namespace, which is imported from
two locations (framework & easyblocks).
This is a well known issue, and there are workaround to just
silence the warning [1,2], but that's probably not the best way
to 'fix' this issue.
We're actually getting it too on our systems, but not
consistently, it depends on how you install EasyBuild (an I
*think* also on the version of setuptools, but I'm not sure about
that).
I've opened an issue on this in the EasyBuild framework
repository on GitHub [3], and tagged it to try and fix this by
the next EasyBuild release.
regards,
Kenneth
[1]
http://stackoverflow.com/questions/7239518/module-pytz-was-already-imported
[2]
http://stackoverflow.com/questions/3861336/how-do-you-correct-module-already-loaded-userwarnings-in-python
[3] https://github.com/hpcugent/easybuild-framework/issues/1588
--
Pablo Escobar López
HPC systems engineer
sciCORE, University of Basel
SIB Swiss Institute of Bioinformatics
http://scicore.unibas.ch
