Shantanu Pavgi wrote:
> 
> 
> I am trying to configure galaxy with sge/drmaa scheduler. The galaxy process 
> is starting up fine without any drmaa configuration. However the galaxy 
> daemon doesn't start properly when I add drmaa configuration lines as shown 
> below. I have set SGE_ROOT and DRMAA_LIBRARY_PATH variables properly. Am I 
> missing something important here?

Could you provide the output of starting Galaxy with the drmaa options
enabled?  You may want to start it in the foreground (without --daemon)
to capture any messages which are not output to paster.log

--nate

> 
> 
> # drmaa configuration: 
> {{{
> start_job_runners = drmaa
> default_cluster_job_runner = drmaa:///
> }}
> 
> 
> # paster.log file - with drmaa config the process dies with "Loaded job 
> runner: galaxy.jobs.runners.local:LocalJobRunner" as last line in the log 
> file. With local job runner the galaxy starts fine as shown below: 
> 
> {{{
> galaxy.jobs DEBUG 2011-05-17 09:59:58,959 Loaded job runner: 
> galaxy.jobs.runners.local:LocalJobRunner
> galaxy.jobs INFO 2011-05-17 09:59:58,959 job manager started
> galaxy.jobs INFO 2011-05-17 09:59:59,325 job stopper started
> galaxy.sample_tracking.external_service_types DEBUG 2011-05-17 09:59:59,330 
> Loaded external_service_type: Simple unknown sequencer 1.0.0
> galaxy.sample_tracking.external_service_types DEBUG 2011-05-17 09:59:59,333 
> Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,349 Enabling 'mobile' 
> controller, class: Mobile
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,417 Enabling 
> 'library_common' controller, class: LibraryCommon
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,435 Enabling 'admin' 
> controller, class: AdminGalaxy
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,451 Enabling 'requests' 
> controller, class: Requests
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,455 Enabling 
> 'external_services' controller, class: ExternalServiceController
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,474 Enabling 'page' 
> controller, class: PageController
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,480 Enabling 
> 'visualization' controller, class: VisualizationController
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,549 Enabling 'tracks' 
> controller, class: TracksController
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,550 Enabling 
> 'requests_common' controller, class: RequestsCommon
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,556 Enabling 
> 'request_type' controller, class: RequestType
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,561 Enabling 
> 'external_service' controller, class: ExternalService
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,562 Enabling 'library' 
> controller, class: Library
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,746 Enabling 'workflow' 
> controller, class: WorkflowController
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,752 Enabling 
> 'library_admin' controller, class: LibraryAdmin
> galaxy.web.framework.base DEBUG 2011-05-17 09:59:59,756 Enabling 'async' 
> controller, class: ASync
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,026 Enabling 'history' 
> controller, class: HistoryController
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,031 Enabling 'error' 
> controller, class: Error
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,090 Enabling 
> 'requests_admin' controller, class: RequestsAdmin
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,095 Enabling 'ucsc_proxy' 
> controller, class: UCSCProxy
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,104 Enabling 'forms' 
> controller, class: Forms
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,137 Enabling 'dataset' 
> controller, class: DatasetInterface
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,143 Enabling 
> 'tool_runner' controller, class: ToolRunner
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,148 Enabling 'tag' 
> controller, class: TagsController
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,158 Enabling 'user' 
> controller, class: User
> galaxy.web.framework.base DEBUG 2011-05-17 10:00:00,165 Enabling 'root' 
> controller, class: RootController
> galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,189 Enabling 'httpexceptions' 
> middleware
> galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,195 Enabling 'recursive' 
> middleware
> galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,220 Enabling 'print debug' 
> middleware
> /share/apps/galaxy/shantanu-temp-workspace/galaxy-cluster-test/galaxy-dist-50e249442c5a/eggs/WebError-0.8a-py2.6.egg/weberror/exceptions/serial_number_generator.py:11:
>  DeprecationWarning: the md5 module is deprecated; use hashlib instead
>   import md5
> galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,726 Enabling 'eval exceptions' 
> middleware
> galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,740 Enabling 'trans logger' 
> middleware
> galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,740 Enabling 'config' middleware
> galaxy.web.buildapp DEBUG 2011-05-17 10:00:00,744 Enabling 'x-forwarded-host' 
> middleware
> Starting server in PID 10170.
> serving on 0.0.0.0:8081 view at http://127.0.0.1:8081
> 
> }}}
> 
> 
> --
> Thanks,
> Shantanu.
> ___________________________________________________________
> 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/
___________________________________________________________
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/

Reply via email to