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 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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