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
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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Louise-Amélie Schmitt