Load balancing and job configuration
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
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/ aebrenne@uci.edu On Thu, May 2, 2013 at 9:00 AM, Olivier Inizan <olivier.inizan@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
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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.Inizan@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/ aebrenne@uci.edu
On Thu, May 2, 2013 at 9:00 AM, Olivier Inizan <olivier.inizan@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/
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participants (2)
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Adam Brenner -
Olivier Inizan