On Wed, May 18, 2011 at 6:56 PM, Marina Gourtovaia <mg8@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
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