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

# ---- Custom Parameters ----------------------------------------------------