On 04/04/2019 15:45, Loris Bennett wrote:
Dear Kenneth,
Kenneth Hoste <[email protected]> writes:
[snip (94 lines)]
If you're not using PythonBundle to install this bundle of Python packages (you
should be if you're not), then you have to ensure that the generated module file
updates $PYTHONPATH...
You can do so using:
modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
in the easyconfig file (or by using PythonBundle which does it for you).
We need better documentation on writing easyconfig files for (bundles of) Python
packages, I hope to get to that soon...
OK, thanks for the help. I have switched from Bundle to PythonBundle
and now get the error:
== 2019-04-04 15:11:23,717 run.py:192 INFO running cmd: export
PYTHONPATH=/tmp/eb-6Ofbuc/tmp8kccPT/lib/python2.7/site-packages:$PYTHONPATH &&cd ..
&& /trinity/shared/easybuild/software/Python/2.7.15-foss-2018b/bin/python -c 'import
numpy; import scipy; scipy.test(verbose=2)'
== 2019-04-04 15:11:23,952 build_log.py:162 ERROR EasyBuild crashed with an error (at
easybuild/software/EasyBuild/3.8.1/lib/python2.7/site-packages/vsc_base-2.8.3-py2.7.egg/vsc/utils/exceptions.py:124
in __init__): cmd "export
PYTHONPATH=/tmp/eb-6Ofbuc/tmp8kccPT/lib/python2.7/site-packages:$PYTHONPATH &&cd .. &&
/trinity/shared/easybuild/software/Python/2.7.15-foss-2018b/bin/python -c 'import numpy; import scipy;
scipy.test(verbose=2)'" exited with exit code 1 and output:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File
"/tmp/eb-6Ofbuc/tmp8kccPT/lib/python2.7/site-packages/scipy-1.1.0-py2.7-linux-x86_64.egg/scipy/_lib/_testutils.py",
line 31, in __call__
import pytest
ImportError: No module named pytest
I would assume this is just a dependency that I need to add to the list of
extensions, but when I mistakenly installed a whole Python along with
the extensions, I didn't see this error.
Is scipy.test part of some selftest within scipy, or is it something
EasyBuild is initiating?
EasyBuild (well, the scipy easyblock included in EasyBuild, I should
say) calls scipy.test when installing the scipy extension, to make sure
it works correctly.
Are you using a stock easyconfig file for Python here?
In any case, you're indeed missing the 'pytest' extension for some
reason, which is required for the scipy tests (apparently)...
regards,
Kenneth
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email [email protected]
