Hi Marina, Thanks... so are you using 1.0.3 instead of 1.0.4?
best, leandro On Wed, May 18, 2011 at 6:56 PM, Marina Gourtovaia <m...@sanger.ac.uk> wrote: > Hi Leandro > > From our previous correspondence I remember that you are using LSF > This is some sort of a bug in the latest drmaa-lsf binding. I moved to the > previous version and everything is OK for me > > Marina > > > On 18/05/2011 16:15, Leandro Hermida wrote: > > Hi all, > > I enabled DRMAA on my test Galaxy server installation and in the server > startup output I get the following strange "E #14ca [ 1.10] * wait > thread: <1002:Not enough memory.>" lines after loading the job manager: > > ... > galaxy.jobs.runners.local INFO 2011-05-18 17:10:23,025 starting workers > galaxy.jobs.runners.local DEBUG 2011-05-18 17:10:23,026 5 workers ready > galaxy.jobs DEBUG 2011-05-18 17:10:23,026 Loaded job runner: > galaxy.jobs.runners.local:LocalJobRunner > galaxy.jobs.runners.drmaa DEBUG 2011-05-18 17:10:23,130 3 workers ready > galaxy.jobs DEBUG 2011-05-18 17:10:23,130 Loaded job runner: > galaxy.jobs.runners.drmaa:DRMAAJobRunner > galaxy.jobs INFO 2011-05-18 17:10:23,131 job manager started > E #14ca [ 0.00] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.02] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.05] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.07] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.10] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.12] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.15] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.17] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.20] * wait thread: <1002:Not enough memory.> > galaxy.jobs INFO 2011-05-18 17:10:23,373 job stopper started > E #14ca [ 0.22] * wait thread: <1002:Not enough memory.> > galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,383 > Loaded external_service_type: Simple unknown sequencer 1.0.0 > galaxy.sample_tracking.external_service_types DEBUG 2011-05-18 17:10:23,386 > Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,400 Enabling 'admin' > controller, class: AdminGalaxy > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,402 Enabling 'async' > controller, class: ASync > E #14ca [ 0.25] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.27] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,428 Enabling 'dataset' > controller, class: DatasetInterface > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,432 Enabling 'error' > controller, class: Error > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,436 Enabling > 'external_service' controller, class: ExternalService > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,437 Enabling > 'external_services' controller, class: ExternalServiceController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,439 Enabling 'forms' > controller, class: Forms > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,441 Enabling 'history' > controller, class: HistoryController > E #14ca [ 0.30] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,460 Enabling 'library' > controller, class: Library > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,461 Enabling > 'library_admin' controller, class: LibraryAdmin > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,462 Enabling > 'library_common' controller, class: LibraryCommon > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,475 Enabling 'mobile' > controller, class: Mobile > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,478 Enabling 'page' > controller, class: PageController > E #14ca [ 0.32] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,482 Enabling > 'request_type' controller, class: RequestType > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,483 Enabling 'requests' > controller, class: Requests > E #14ca [ 0.35] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,508 Enabling > 'requests_admin' controller, class: RequestsAdmin > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,509 Enabling > 'requests_common' controller, class: RequestsCommon > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,511 Enabling 'root' > controller, class: RootController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,514 Enabling 'tag' > controller, class: TagsController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,519 Enabling > 'tool_runner' controller, class: ToolRunner > E #14ca [ 0.37] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.40] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,558 Enabling 'tracks' > controller, class: TracksController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,562 Enabling > 'ucsc_proxy' controller, class: UCSCProxy > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,564 Enabling 'user' > controller, class: User > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,567 Enabling > 'visualization' controller, class: VisualizationController > E #14ca [ 0.42] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.45] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.47] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.50] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.53] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.55] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.58] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,747 Enabling 'workflow' > controller, class: WorkflowController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,755 Enabling 'contents' > API controller, class: ContentsController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,757 Enabling 'forms' > API controller, class: FormDefinitionAPIController > E #14ca [ 0.60] * wait thread: <1002:Not enough memory.> > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,762 Enabling > 'libraries' API controller, class: LibrariesController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,767 Enabling > 'request_types' API controller, class: RequestTypeAPIController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,768 Enabling 'requests' > API controller, class: RequestsAPIController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,770 Enabling 'roles' > API controller, class: RoleAPIController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,772 Enabling 'samples' > API controller, class: SamplesAPIController > galaxy.web.framework.base DEBUG 2011-05-18 17:10:23,773 Enabling 'users' > API controller, class: UserAPIController > E #14ca [ 0.63] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.65] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.67] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.70] * wait thread: <1002:Not enough memory.> > galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,862 Enabling 'httpexceptions' > middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,869 Enabling 'remote user' > middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,871 Enabling 'recursive' > middleware > E #14ca [ 0.72] * wait thread: <1002:Not enough memory.> > galaxy.web.buildapp DEBUG 2011-05-18 17:10:23,882 Enabling 'print debug' > middleware > E #14ca [ 0.74] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.77] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.79] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.82] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.85] * wait thread: <1002:Not enough memory.> > /gpfshpc/home/lhermida/soft/galaxy/galaxy_dist/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 > E #14ca [ 0.87] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.90] * wait thread: <1002:Not enough memory.> > galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,058 Enabling 'eval > exceptions' middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,062 Enabling 'trans logger' > middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,062 Enabling 'config' > middleware > galaxy.web.buildapp DEBUG 2011-05-18 17:10:24,064 Enabling > 'x-forwarded-host' middleware > Starting server in PID 5229. > serving on http://10.155.10.23:8082 > E #14ca [ 0.92] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.95] * wait thread: <1002:Not enough memory.> > E #14ca [ 0.97] * wait thread: <1002:Not enough memory.> > ... > > Do I need to increase some kind of running memory somewhere or is it > another problem? > > thanks, > Leandro > > > ___________________________________________________________ > 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/ > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a company > registered in England with number 2742969, whose registered office is 215 > Euston Road, London, NW1 2BE. > > ___________________________________________________________ > 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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