Galaxy-Condor Permission Denied

Question: Galaxy-Condor Permission Denied

7.2 years ago by

Oren Livne • 130

Oren Livne • 130 wrote:

Dear All, I am using Galaxy with condor as the scheduler via the DRMAA Job Runner. on Debian 6. Jobs are submitted to COndor but they are held because of permissions: condor@vm-debian:~$ condor_q -analyze 10.0 -- Submitter: vm-debian.uchad.uchospitals.edu : <165.68.219.43:40312> : vm-debian.uchad.uchospitals.edu 010.000: Request is held. Hold reason: Error from vm-debian.uchad.uchospitals.edu: Failed to open '/home/galaxy/galaxy-dist/database/pbs/19.o' as standard output: Permission denied (errno 13) condor@vm-debian:~$ ls -l /home/galaxy/galaxy-dist/database/pbs/19.o -rw-r--r-- 1 galaxy galaxy 0 Oct 4 16:40 /home/galaxy/galaxy-dist/database/pbs/19.o I am running galaxy as the galaxy user. I also have a condor user. How to ensure that jobs are submitted as the proper user? Thanks so much, Oren

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modified 7.2 years ago by Nathan Panike • 40 • written 7.2 years ago by Oren Livne • 130

7.2 years ago by

Nathan Panike • 40

Nathan Panike • 40 wrote:

You might want to ask about this on condor-users@cs.wisc.edu, if it is a Condor problem. (cc'd) Which user does condor believe you to be?

ADD COMMENT • link written 7.2 years ago by Nathan Panike • 40

Dear Nick, Haven't heard back yet from condor, I found in previous posts and condor docs that this might have to do with the condor UID_DOMAIN config variable, which is set to $(FULL_HOSTNAME) in my case, as recommended therein. Also, "condor_master" is being run as root. The user running the "condor_submit" command is "galaxy", which has permissions to write that output file. But I don't know if this is the relevant uid or if condor is trying to open that file as a different user within the condor_submit command. Oren

ADD REPLY • link written 7.2 years ago by Oren Livne • 130

7.2 years ago by

Nathan Panike • 40

Nathan Panike • 40 wrote:

What is the output of the following? condor_q -f '%s\n' FileSystemDomain <job> condor_q -f '%s\n' Owner <job> condor_q -f '%s\n' User <job> Nathan Panike

ADD COMMENT • link written 7.2 years ago by Nathan Panike • 40

Dear Nathan, Thank you so much for your help. condor@vm-debian:/home/galaxy/galaxy-dist/database/pbs$ condor_q -- Submitter: vm-debian.uchad.uchospitals.edu : <165.68.219.43:56855> : vm-debian.uchad.uchospitals.edu ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD 18.0 galaxy 10/5 12:01 0+00:00:01 H 0 0.0 galaxy_31.sh 1 jobs; 0 idle, 0 running, 1 held condor@vm-debian:/home/galaxy/galaxy-dist/database/pbs$ condor_q -f '%s\n' FileSystemDomain 18.0 uchad.uchospitals.edu condor@vm-debian:/home/galaxy/galaxy-dist/database/pbs$ condor_q -f '%s\n' Owner 18.0 galaxy condor@vm-debian:/home/galaxy/galaxy-dist/database/pbs$ condor_q -f '%s\n' User 18.0 galaxy@uchad.uchospitals.edu We added the condor to the galaxy user group, but that didn't help. Oren

ADD REPLY • link written 7.2 years ago by Oren Livne • 130

Dear Nathan, We found that condor was running the job as the "nobody" user, which had no permissions to the files galaxy created in the database/pbs directory. This was fixed by setting TRUST_UID_DOMAIN = True in the condor config file. Now the job runs, but fails immediately because it cannot find the PATH environment variable. If I run the generated database/pbs/galaxy_<jobid>.sh file manually at the command line, it works fine. Do we need any some environment setting in galaxy/condor? Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/stats/column_maker.py", line 7, in <module> from galaxy.tools import validation File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 15, in <module> from galaxy import util, jobs, model File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 4, in <module> from galaxy import util, model File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in <module> import galaxy.datatypes.registry File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 6, in <module> import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/data.py", line 7, in <module> import metadata File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py", line 5, in <module> from galaxy.web import form_builder File "/home/galaxy/galaxy-dist/lib/galaxy/web/__init__.py", line 5, in <module> from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder, expose_api File "/home/galaxy/galaxy- dist/lib/galaxy/web/framework/__init__.py", line 18, in <module> import helpers File "/home/galaxy/galaxy- dist/lib/galaxy/web/framework/helpers/__init__.py", line 4, in <module> from webhelpers import * File "/home/galaxy/galaxy- dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/__init__.py", line 1, in <module> from webhelpers.rails import * File "/home/galaxy/galaxy- dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/rails/__init__.py", line 9, in <module> from text import * File "/home/galaxy/galaxy- dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/rails/text.py", line 10, in <module> import webhelpers.textile as textile File "/home/galaxy/galaxy- dist/eggs/WebHelpers-0.2-py2.6.egg/webhelpers/textile.py", line 241, in <module> import tidy File "/usr/lib/pymodules/python2.6/tidy/__init__.py", line 43, in <module> from tidy.lib import parse, parseString File "/usr/lib/pymodules/python2.6/tidy/lib.py", line 24, in <module> os.environ['PATH'] = "%s%s%s" % (packagedir, os.pathsep, os.environ['PATH']) File "/usr/lib/python2.6/UserDict.py", line 22, in __getitem__ raise KeyError(key) KeyError: 'PATH' Thank you so much again for your help. Oren

ADD REPLY • link written 7.2 years ago by Oren Livne • 130

7.2 years ago by

Nathan Panike • 40

Nathan Panike • 40 wrote:

You can set the environment by using an "environment = " command in the submit file or, if appropriate, you can copy your environment to the job by inserting "getenv = true" in the submit file. This is described in the condor manual at http://www.cs.wisc.edu/condor/manual/v7.7/2_5Submitting_Job.html#2516 You're welcome Nathan Panike

ADD COMMENT • link written 7.2 years ago by Nathan Panike • 40

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