Re: [galaxy-dev] Error after migrating to latest changeset
michael burrell (TSL) wrote: > Good Morning Nate, > > Thanks for the response, I was not able to find a work around for this so > we redeployed a fresh version of galaxy. Any ideas what could have caused > this issue ? It looks like a database migration had failed but still incremented the database version. If you still have the database we could double check, although it may not be possible to determine how it happened regardless. --nate > > Thanks > > Michael. > > On 16/08/2011 20:05, "Nate Coraor" wrote: > > >michael burrell (TSL) wrote: > >> Good Morning, > >> > >> I am getting a big problem with our production server when I upgrade to > >>the latest change set (it was quite out of date). I have attached quite > >>a long paster output to try and show whats going on, > >> > >> Our galaxy instance no longer seems to run jobs at all, they are not > >>allocated a job runner and the following is given in the paster log > >> > >> I look forwards to your assistance. > > > >Hi Michael, > > > >Sorry for the delay in response. Did you ever find a solution to your > >problem, or are you still experiencing it? > > > >Thanks, > >--nate > > > >> > >> Thanks > >> > >> Michael. > >> == > >> > >> galaxy.datatypes.registry DEBUG 2011-07-12 11:46:50,433 Loaded indexer: > >>INDEXER_Interval_0 > >> galaxy.jobs.runners.local INFO 2011-07-12 11:46:50,436 starting workers > >> galaxy.jobs.runners.local DEBUG 2011-07-12 11:46:50,437 5 workers ready > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,438 Loaded job runner: > >>galaxy.jobs.runners.local:LocalJobRunner > >> galaxy.jobs.runners.drmaa DEBUG 2011-07-12 11:46:50,483 10 workers ready > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,483 Loaded job runner: > >>galaxy.jobs.runners.drmaa:DRMAAJobRunner > >> galaxy.jobs INFO 2011-07-12 11:46:50,484 job manager started > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,861 no runner: 4400 is still in > >>new state, adding to the jobs queue > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4401 is still in > >>new state, adding to the jobs queue > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4403 is still in > >>new state, adding to the jobs queue > >> galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4404 is still in > >>new state, adding to the jobs queue > >> galaxy.jobs INFO 2011-07-12 11:46:50,869 job stopper started > >> galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 > >>11:46:50,872 Loaded external_service_type: Simple unknown sequencer 1.0.0 > >> galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 > >>11:46:50,875 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,895 Enabling > >>'admin' controller, class: AdminGalaxy > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,898 Enabling > >>'async' controller, class: ASync > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,915 Enabling > >>'dataset' controller, class: DatasetInterface > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,917 Enabling > >>'error' controller, class: Error > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,920 Enabling > >>'forms' controller, class: Forms > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,924 Enabling > >>'history' controller, class: HistoryController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,942 Enabling > >>'library' controller, class: Library > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,946 Enabling > >>'library_admin' controller, class: LibraryAdmin > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,947 Enabling > >>'library_common' controller, class: LibraryCommon > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,949 Enabling > >>'mobile' controller, class: Mobile > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,952 Enabling 'page' > >>controller, class: PageController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,958 Enabling > >>'requests' controller, class: Requests > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,996 Enabling > >>'requests_admin' controller, class: RequestsAdmin > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,997 Enabling > >>'requests_common' controller, class: RequestsCommon > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,000 Enabling 'root' > >>controller, class: RootController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,002 Enabling 'tag' > >>controller, class: TagsController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,004 Enabling > >>'tool_runner' controller, class: ToolRunner > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,013 Enabling > >>'tracks' controller, class: TracksController > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,016 Enabling > >>'ucsc_proxy' controller, class: UCSCProxy > >> galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,019 Enabling 'user' > >>controller, class: User > >> galaxy.web.framework.base DEBUG 2011-
Re: [galaxy-dev] Error after migrating to latest changeset
michael burrell (TSL) wrote: > Good Morning, > > I am getting a big problem with our production server when I upgrade to the > latest change set (it was quite out of date). I have attached quite a long > paster output to try and show whats going on, > > Our galaxy instance no longer seems to run jobs at all, they are not > allocated a job runner and the following is given in the paster log > > I look forwards to your assistance. Hi Michael, Sorry for the delay in response. Did you ever find a solution to your problem, or are you still experiencing it? Thanks, --nate > > Thanks > > Michael. > == > > galaxy.datatypes.registry DEBUG 2011-07-12 11:46:50,433 Loaded indexer: > INDEXER_Interval_0 > galaxy.jobs.runners.local INFO 2011-07-12 11:46:50,436 starting workers > galaxy.jobs.runners.local DEBUG 2011-07-12 11:46:50,437 5 workers ready > galaxy.jobs DEBUG 2011-07-12 11:46:50,438 Loaded job runner: > galaxy.jobs.runners.local:LocalJobRunner > galaxy.jobs.runners.drmaa DEBUG 2011-07-12 11:46:50,483 10 workers ready > galaxy.jobs DEBUG 2011-07-12 11:46:50,483 Loaded job runner: > galaxy.jobs.runners.drmaa:DRMAAJobRunner > galaxy.jobs INFO 2011-07-12 11:46:50,484 job manager started > galaxy.jobs DEBUG 2011-07-12 11:46:50,861 no runner: 4400 is still in new > state, adding to the jobs queue > galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4401 is still in new > state, adding to the jobs queue > galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4403 is still in new > state, adding to the jobs queue > galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4404 is still in new > state, adding to the jobs queue > galaxy.jobs INFO 2011-07-12 11:46:50,869 job stopper started > galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 11:46:50,872 > Loaded external_service_type: Simple unknown sequencer 1.0.0 > galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 11:46:50,875 > Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,895 Enabling 'admin' > controller, class: AdminGalaxy > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,898 Enabling 'async' > controller, class: ASync > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,915 Enabling 'dataset' > controller, class: DatasetInterface > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,917 Enabling 'error' > controller, class: Error > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,920 Enabling 'forms' > controller, class: Forms > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,924 Enabling 'history' > controller, class: HistoryController > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,942 Enabling 'library' > controller, class: Library > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,946 Enabling > 'library_admin' controller, class: LibraryAdmin > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,947 Enabling > 'library_common' controller, class: LibraryCommon > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,949 Enabling 'mobile' > controller, class: Mobile > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,952 Enabling 'page' > controller, class: PageController > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,958 Enabling 'requests' > controller, class: Requests > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,996 Enabling > 'requests_admin' controller, class: RequestsAdmin > galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,997 Enabling > 'requests_common' controller, class: RequestsCommon > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,000 Enabling 'root' > controller, class: RootController > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,002 Enabling 'tag' > controller, class: TagsController > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,004 Enabling > 'tool_runner' controller, class: ToolRunner > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,013 Enabling 'tracks' > controller, class: TracksController > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,016 Enabling 'ucsc_proxy' > controller, class: UCSCProxy > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,019 Enabling 'user' > controller, class: User > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,022 Enabling > 'visualization' controller, class: VisualizationController > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,107 Enabling 'workflow' > controller, class: WorkflowController > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,110 Enabling > 'external_service' controller, class: ExternalService > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,112 Enabling > 'external_services' controller, class: ExternalServiceController > galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,115 Enabling > 'request_type' controller, class: RequestType > galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,146 Enabling 'httpexceptions' > middleware > galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,1
