wait thread: <1002:Not enough memory.> error after enabling DRMAA
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
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 <http://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 <http://galaxy.jobs> DEBUG 2011-05-18 17:10:23,130 Loaded job runner: galaxy.jobs.runners.drmaa:DRMAAJobRunner galaxy.jobs <http://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 <http://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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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 <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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Yes. M. On 18/05/2011 18:23, Leandro Hermida wrote:
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 <mg8@sanger.ac.uk <mailto: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 <http://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 <http://galaxy.jobs> DEBUG 2011-05-18 17:10:23,130 Loaded job runner: galaxy.jobs.runners.drmaa:DRMAAJobRunner galaxy.jobs <http://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 <http://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:
-- 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:
-- 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.
participants (2)
-
Leandro Hermida -
Marina Gourtovaia