Hi again
Update, sorry for spamming:
It is not ALL jobs that fail. Only the ones that get dispatched to our
Grid Engine cluster (so nearly all).
The reason appears to be that the path to the Python binary is added to
the PATH variable when the job arrives on the worker node:
[galaxy_hpc@hpc1node25 galaxy-dist]$ export
PATH=/home/galaxy_hpc/galaxy-dist/.venv/bin:/tmp/5000354.1.researchmid.q:/usr/local/bin:/bin:/usr/bin
[galaxy_hpc@hpc1node25 galaxy-dist]$ python
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Python 2.7.6 (default, Oct 25 2017, 12:28:23)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import json
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named json
This is the wrong python to be running there. It should just go with the
one in /usr/bin. If I change PATH, it works fine:
[galaxy_hpc@hpc1node25 galaxy-dist]$ export
PATH=/tmp/5000354.1.researchmid.q:/usr/local/bin:/bin:/usr/bin[galaxy_hpc@hpc1node25
galaxy-dist]$ python
Python 2.6.6 (r266:84292, Aug 9 2016, 06:11:56)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-17)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import json
>>>
Does anyone have an idea how I can stop this from happening? Where is
the PATH set before submitting the job?
Thanks
Ulf
On 25/10/17 15:23, Ulf Schaefer wrote:
Hi all
After running the recommended update I am now on branch 17.09. As part
of the update I set up a new virtual env running an additional python
2.7.6. My previous virtual env was running 2.6.6 which is a system
requirement for Centos 6.
All dependencies were installed and Galaxy starts fine, but no tools
run. The error is always a variation of this:
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Traceback (most recent call last):
File
"galaxy-dist/database/jobs_directory/000/418/418014/set_metadata_4LcsZv.py",
line 1, in <module>
from galaxy_ext.metadata.set_metadata import set_metadata;
set_metadata()
File "galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py", line 19,
in <module>
import json
ImportError: No module named json
I put some debug output at the top of set_metadata.py and it is indeed
running the correct python version from the virtual env. Needless to say
I can import json just fine using that python version. Any ideas?
Any help is greatly appreciated.
Thanks
Ulf
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