Re: [galaxy-dev] Load balancing and job configuration
Thanks Adam when I specify handlers it works fine :)
I also try to add a drmaa plugin and create a new destination:
job_conf
plugins
plugin id=local type=runner
load=galaxy.jobs.runners.local:LocalJobRunner/
plugin id=sge type=runner
load=galaxy.jobs.runners.drmaa:DRMAAJobRunner/
/plugins
handlers default=handlers
handler id=server:handler0 tags=handlers/
handler id=server:handler1 tags=handlers/
/handlers
destinations default=local
destination id=sge_default runner=sge/
destination id=local runner=local/
/destinations
/job_conf
My env var DRMAA_LIBRARY_PATH is set to /usr/lib64/libdrmaa.so.1.0, and
when I restart the instance I have the following error in handler's log
files:
galaxy.jobs.manager DEBUG 2013-05-03 17:06:50,978 Starting job handler
galaxy.jobs.runners DEBUG 2013-05-03 17:06:50,979 Starting 4 LocalRunner
workers
galaxy.jobs DEBUG 2013-05-03 17:06:50,980 Loaded job runner
'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
line 37, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /home/galaxy/galaxy-dist/lib/galaxy/app.py, line 159, in __init__
self.job_manager = manager.JobManager( self )
File /home/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py, line 32, in
__init__
self.job_handler = handler.JobHandler( app )
File /home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 29, in
__init__
self.dispatcher = DefaultJobDispatcher( app )
File /home/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py, line 543, in
__init__
self.job_runners = self.app.job_config.get_job_runner_plugins()
File /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 486,
in get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get(
'kwds', {} ) )
File /home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line
75, in __init__
self.ds.initialize()
File
/home/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py,
line 274, in initialize
_w.init(contactString)
File
/home/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py,
line 59, in init
return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
File
/home/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py,
line 90, in error_check
raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value))
DrmCommunicationException: code 2: range_list containes no elements
Removing PID file handler0.pid
Any ideas ?
Thanks again for your help.
Olivier Inizan
Unité de Recherches en Génomique-Info (UR INRA 1164),
INRA, Centre de recherche de Versailles, bat.18
RD10, route de Saint Cyr
78026 Versailles Cedex, FRANCE
olivier.ini...@versailles.inra.fr
Tél: +33 1 30 83 38 25
Fax: +33 1 30 83 38 99
http://urgi.versailles.inra.fr [urgi.versailles.inra.fr]
Twitter: @OlivierInizan
On Thu, 2 May 2013, Adam Brenner wrote:
Oliver,
The new job running file is also providing me a lot of headaches. The
documentation on site is correct, but some of the items are not yet
implemented, for example, DRMAA external scripts still need to be in
the universe_wsgi.ini, yet the site say to put them in job_conf.xml
file! Lot of hair pulling and waiting response from IRC to figure this
out...wasn't fun.
As for your issue, you want to specify your handlers, not your
webserver for your handler types.
handler id=handler0 tags=handlers/
handler id=handler1 tags=handlers/
Let me know if this helps,
-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/
aebre...@uci.edu
On Thu, May 2, 2013 at 9:00 AM, Olivier Inizan
olivier.ini...@versailles.inra.fr wrote:
Dear galaxy-dev-list,
I am trying to use new-style job configuration whith a load-balancing on 2
web servers and 2 job hanlders.
I have configured load balancing as follows (universe_wsgi.ini):
# Configuration of the internal HTTP server.
[server:web0]
use = egg:Paste#http
port = 8083
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 7
[server:web1]
use = egg:Paste#http
port = 8082
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 7
[server:manager]
use = egg:Paste#http
port = 8079
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
[server:handler0]
use = egg:Paste#http
port = 8090
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
[server:handler1]
use = egg:Paste#http
port = 8091
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
This configuration works fine (manager.log):
galaxy.jobs.manager DEBUG 2013-04-23 12:20:22,901 Starting job handler
galaxy.jobs.runners DEBUG 2013-04-23 12:20:22,902
Re: [galaxy-dev] Load balancing and job configuration
Oliver, The new job running file is also providing me a lot of headaches. The documentation on site is correct, but some of the items are not yet implemented, for example, DRMAA external scripts still need to be in the universe_wsgi.ini, yet the site say to put them in job_conf.xml file! Lot of hair pulling and waiting response from IRC to figure this out...wasn't fun. As for your issue, you want to specify your handlers, not your webserver for your handler types. handler id=handler0 tags=handlers/ handler id=handler1 tags=handlers/ Let me know if this helps, -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/ aebre...@uci.edu On Thu, May 2, 2013 at 9:00 AM, Olivier Inizan olivier.ini...@versailles.inra.fr wrote: Dear galaxy-dev-list, I am trying to use new-style job configuration whith a load-balancing on 2 web servers and 2 job hanlders. I have configured load balancing as follows (universe_wsgi.ini): # Configuration of the internal HTTP server. [server:web0] use = egg:Paste#http port = 8083 host = 127.0.0.1 use_threadpool = true threadpool_workers = 7 [server:web1] use = egg:Paste#http port = 8082 host = 127.0.0.1 use_threadpool = true threadpool_workers = 7 [server:manager] use = egg:Paste#http port = 8079 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8090 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8091 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 This configuration works fine (manager.log): galaxy.jobs.manager DEBUG 2013-04-23 12:20:22,901 Starting job handler galaxy.jobs.runners DEBUG 2013-04-23 12:20:22,902 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2013-04-23 12:20:22,904 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners DEBUG 2013-04-23 12:20:22,909 Starting 3 LWRRunner workers galaxy.jobs DEBUG 2013-04-23 12:20:22,911 Loaded job runner 'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr' galaxy.jobs DEBUG 2013-04-23 12:20:22,911 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2013-04-23 12:20:22,911 Loaded job runners plugins: lwr:local galaxy.jobs.handler INFO 2013-04-23 12:20:22,912 job handler stop queue started galaxy.jobs.handler INFO 2013-04-23 12:20:22,919 job handler queue started To use new-style job configuration I have create the following job_conf.xml: ?xml version=1.0? !-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -- job_conf plugins plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner/ /plugins handlers default=handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. -- handler id=server:web0 tags=handlers/ handler id=server:web1 tags=handlers/ /handlers destinations default=local destination id=local runner=local/ /destinations /job_conf When I restart the instance the manager.log outputs: galaxy.jobs DEBUG 2013-05-02 17:25:28,402 Loading job configuration from ./job_conf.xml galaxy.jobs DEBUG 2013-05-02 17:25:28,402 Read definition for handler 'server:web0' galaxy.jobs DEBUG 2013-05-02 17:25:28,403 Read definition for handler 'server:web1' galaxy.jobs DEBUG 2013-05-02 17:25:28,403 handlers default set to child with id or tag 'handlers' galaxy.jobs DEBUG 2013-05-02 17:25:28,403 destinations default set to child with id or tag 'local' galaxy.jobs DEBUG 2013-05-02 17:25:28,403 Done loading job configuration So everything seems fine but when I try to run a tool, the corresponding job is in permanent waiting status (gray color in history). I think I have missed something in the configuration process, Thanks for your help, Olivier ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
