On Jun 21, 2012, at 4:50 PM, Dorset, Daniel C wrote:

I have galaxy running on my institution’s cluster computing service, which uses PBS. It’s in a balanced configuration.

Jobs going to the cluster submit without any problem at all. However, any job that I have specified to run locally in the universe_wgsi.ini file won’t dispatch. There isn’t any record of the job in the manager.log, or any of the handler[#].log files. In fact, I’ve never seen anything in the handler logfiles after “serving on [GALAXY IP]:[SPECIFIC PORT NUMBER OF HANDLER]”. The manager logfile has all the details about the jobs dispatched to the pbs runner, but nothing about local jobs.

HOWEVER, if I stop Galaxy using “GALAXY_RUN_ALL=1 sh ./run.sh --stop-daemon” and restart using “GALAXY_RUN_ALL=1 sh ./run.sh --daemon” then the local jobs that were waiting to run begin immediately. Information about them shows up in manager.log, but not in the handler0.log or handler1.log files.

I’m on an 8-core Dell R410 server, if that matters.

The server portion of my universe_wsgi.ini file is pasted below.

# ---- HTTP Server ----------------------------------------------------------

# Configuration of the internal HTTP server.

[server:web0]

# The internal HTTP server to use. Currently only Paste is provided. This # option is required. use = egg:Paste#http

# The port on which to listen. port = 8080

# The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. host = localhost

# Use a threadpool for the web server instead of creating a thread for each # request. use_threadpool = True

# Number of threads in the web server thread pool. threadpool_workers = 7

[server:web1] use = egg:Paste#http port = 8081 host = localhost use_threadpool = true threadpool_workers = 7

[server:manager] use = egg:Paste#http port = 8079 host = localhost use_threadpool = true threadpool_workers = 5

[server:handler0] use = egg:Paste#http port = 8090 host = localhost use_threadpool = true threadpool_workers = 5

[server:handler1] use = egg:Paste#http port = 8091 host = localhost use_threadpool = true threadpool_workers = 5

[app:main]

# -- Application and filtering

job_manager = manager job_handler = handler0,handler1

Hi Daniel,

This parameter should be 'job_handlers'

Are there any entries in your [galaxy:tool_handlers] and/or [galaxy:tool_runners] sections?

--nate

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On Jun 22, 2012, at 12:26 PM, Dorset, Daniel C wrote:

Good catch, thanks Nate! I have plenty of tool_runners defined, but no tool_handlers. Do I have to specifically assign tool handlers in order for them to be used in job deployment?

No, if you don't define any specific handlers in the [galaxy:tool_handlers], each job will have one assigned randomly from the list in the 'job_handers' parameter in [app:main].

--nate

Thanks!

Dan

...

Hi Daniel,

This parameter should be 'job_handlers'

Are there any entries in your [galaxy:tool_handlers] and/or [galaxy:tool_runners] sections?

--nate