Mmm... for some reason LD_LIBRARY_PATH was ignored but it looks like
it's working fine when I set the lib path in a .conf file in
/etc/ld.so.conf.d/
Hopefully it'll not break again :)
Best,
L-A
Le 19/04/2012 17:19, Louise-Amélie Schmitt a écrit :
Hi everyone,
I'm currently trying to set up our local Galaxy so it can run jobs as
the real user. I followed the documentation and set the galaxy user as
a sudoer. However, I get an error message whenever I'm trying to run a
job:
galaxy.jobs.runners.drmaa ERROR 2012-04-19 14:57:48,376 Uncaught
exception queueing job
Traceback (most recent call last):
File /g/funcgen/galaxy-dev/lib/galaxy/jobs/runners/drmaa.py, line
133, in run_next
self.queue_job( obj )
File /g/funcgen/galaxy-dev/lib/galaxy/jobs/runners/drmaa.py, line
219, in queue_job
job_id = self.external_runjob(filename,
job_wrapper.user_system_pwent[2]).strip()
File /g/funcgen/galaxy-dev/lib/galaxy/jobs/runners/drmaa.py, line
427, in external_runjob
raise RuntimeError(External_runjob failed (exit code %s)\nCalled
from %s:%d\nChild process reported error:\n%s % (str(exitcode),
__filename__(), __lineno__(), stderrdata))
RuntimeError: External_runjob failed (exit code 127)
Called from /g/funcgen/galaxy-dev/lib/galaxy/jobs/runners/drmaa.py:427
Child process reported error:
python: error while loading shared libraries: libpython2.6.so.1.0:
cannot open shared object file: No such file or directory
Looking closely, it's the non-root user it tries to switch to that
doesn't have the LD_LIBRARY_PATH properly set, so there should be an
environment inheritance issue. However, I tried to print stuff from
the scripts/drmaa_external_runner.py script in EVERY WAY I could think
of, to no avail. As if it doesn't even run. Which is surprising since
root can run python properly, so it really looks like it's really
changing users.
I really fail to see where the problem could come from, so if you have
leads to suggest, I'll be forever grateful.
Best,
L-A
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