Hi Mariusz, In another Galaxy post Marina had mentioned it is a bug with the latest FedStage LSF DRMAA 1.0.4 implementation.
If you build and use the previous 1.0.3 version it works fine and you don't get this error. regards, Leandro 2011/5/19 Mariusz Mamoński <mamon...@man.poznan.pl> > Hi, > > > ------------------------------ > > > > Message: 13 > > Date: Wed, 18 May 2011 17:15:06 +0200 > > From: Leandro Hermida <soft...@leandrohermida.com> > > To: Galaxy Dev <galaxy-...@bx.psu.edu> > > Subject: [galaxy-dev] wait thread: <1002:Not enough memory.> error > > after enabling DRMAA > > Message-ID: <BANLkTi=J4-ct04U=8dm6ra=sjcr_ede...@mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > 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 > > > are you using LSF? > > > > 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? > > i think it is a bug. Could you try to edit the > > LSF_TOP/conf/lsf_drmaa.conf > > and set there > > wait_thread: 0 > > ? > > Unfortunately i do not have access to any LSF cluster so i can not dig > further into this problem. > > > > > thanks, > > Leandro > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20110518/7dd7663d/attachment-0001.html > > > > > > ------------------------------ > > > > _______________________________________________ > > galaxy-dev mailing list > > galaxy-dev@lists.bx.psu.edu > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > > > End of galaxy-dev Digest, Vol 59, Issue 17 > > ****************************************** > > > > > Cheers, > -- > Mariusz >
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