Run Jobs as Real User - Unable to get working with Drmaa (SGE) and job_conf.xml
I have the following job_conf.xml file setup for our cluster: http://pastebin.com/raw.php?i=0uNhcVJk When running jobs from my admin account via Galaxy it runs under the same user as galaxy is, for testing, this as root. I need for it to run under the real user. The email address / galaxy account I am using to test with does match with a user on the cluster -- user@example.com where user is a valid user account with correct permissions to run jobs on our cluster and queue. I followed the information here: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jo... Any ideas as to why galaxy_external* is not being called? The paster.log file does not show anything useful regarding calling external scripts. -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu
Anyone have any ideas as to why its not running? Surely must be a few users who run Galaxy via a Scheduler using DRMAA... My updated job_conf.xml is like so: http://pastebin.com/raw.php?i=QJbay57i Jobs do get submitted to DRMAA, but the scripts are never called to run as real user. I have DEBUG set to true in universe_wsgi.ini and nothing regarding errors or debug message are created in paster.log about this. -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu On Tue, Apr 16, 2013 at 4:55 PM, Adam Brenner <aebrenne@uci.edu> wrote:
I have the following job_conf.xml file setup for our cluster: http://pastebin.com/raw.php?i=0uNhcVJk
When running jobs from my admin account via Galaxy it runs under the same user as galaxy is, for testing, this as root. I need for it to run under the real user.
The email address / galaxy account I am using to test with does match with a user on the cluster -- user@example.com where user is a valid user account with correct permissions to run jobs on our cluster and queue.
I followed the information here: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jo...
Any ideas as to why galaxy_external* is not being called? The paster.log file does not show anything useful regarding calling external scripts.
-- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences
Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/
University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu
Okay! I found out what the issue was. I am not sure if this is related to the new Galaxy setup (requiring job_conf.xml) but, I added the following lines to my universe_wsgi.ini, saved, restarted and it worked. drmaa_external_runjob_script = scripts/drmaa_external_runner.py drmaa_external_killjob_script = scripts/drmaa_external_killer.py external_chown_script = scripts/external_chown_script.py So the bigger question is: Is the current documentation wrong and adding drmaa to the job_conf.xml incorrect? If not, then what I am doing wrong in my file? Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu On Tue, Apr 23, 2013 at 10:47 AM, Adam Brenner <aebrenne@uci.edu> wrote:
Anyone have any ideas as to why its not running? Surely must be a few users who run Galaxy via a Scheduler using DRMAA...
My updated job_conf.xml is like so: http://pastebin.com/raw.php?i=QJbay57i
Jobs do get submitted to DRMAA, but the scripts are never called to run as real user. I have DEBUG set to true in universe_wsgi.ini and nothing regarding errors or debug message are created in paster.log about this.
-- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences
Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/
University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu
On Tue, Apr 16, 2013 at 4:55 PM, Adam Brenner <aebrenne@uci.edu> wrote:
I have the following job_conf.xml file setup for our cluster: http://pastebin.com/raw.php?i=0uNhcVJk
When running jobs from my admin account via Galaxy it runs under the same user as galaxy is, for testing, this as root. I need for it to run under the real user.
The email address / galaxy account I am using to test with does match with a user on the cluster -- user@example.com where user is a valid user account with correct permissions to run jobs on our cluster and queue.
I followed the information here: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Submitting_Jo...
Any ideas as to why galaxy_external* is not being called? The paster.log file does not show anything useful regarding calling external scripts.
-- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences
Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/
University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu
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Adam Brenner