[ome-users] Unable to import image files
José Salavert Torres
josator at ebi.ac.uk
Tue Mar 24 16:44:17 GMT 2015
I have tried that removed all logs and now I get rid of that error, but import is still not working.
master.err shows that libblas is missing once but it also was before, import worked but slowly.
I try to import many times but this error only appears once at startup on the master log.
No other error is present in the master logs.
I think this has been caused by an abnormal interruption of "omero admin stop”.
We are installing it and see what happens.
I tried an import looking at the logs, this is what appears at Blitz-0.log:
2015-03-24 16:36:16,724 INFO [ omero.cmd.SessionI] (Server-118) Removed servant from adapter: 3ce5b4b7-8fb0-4048-b21b-5605cc977e72omero.api.IAdmin
2015-03-24 16:36:33,330 INFO [ ome.services.blitz.fire.SessionManagerI] (Server-120) Found session locally: c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:33,332 INFO [ ome.services.blitz.fire.SessionManagerI] (Server-120) Rejoining session ServiceFactoryI(session-e83a7dc9-30c6-4bd3-a23c-735adfe52b02/c8e1208f-31bc-405c-90d0-b580515a00e8) (agent=OMERO.sessions)
2015-03-24 16:36:33,336 INFO [ omero.cmd.SessionI] (Server-119) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/e83a7dc9-30c6-4bd3-a23c-735adfe52b02omero.api.IAdmin(omero.api._IAdminTie at 15e17e04)
2015-03-24 16:36:33,337 INFO [ ome.services.util.ServiceHandler] (Server-120) Meth: interface ome.api.IAdmin.getEventContext
2015-03-24 16:36:33,337 INFO [ ome.services.util.ServiceHandler] (Server-120) Args: ()
2015-03-24 16:36:33,340 INFO [ ome.security.basic.EventHandler] (Server-120) Auth: user=0,group=0,event=null(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:33,340 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[c8e1208f-31bc-405c-90d0-b580515a00e8]
2015-03-24 16:36:33,340 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Args: [null, InternalSF at 727982057]
2015-03-24 16:36:33,342 INFO [ ome.security.basic.EventHandler] (3-thread-4) Auth: user=0,group=0,event=null(Sessions),sess=afe0ab3d-4f54-47c2-91e8-487d111d9f63
2015-03-24 16:36:33,349 INFO [ org.perf4j.TimingLogger] (3-thread-4) start[1427214993340] time[9] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2015-03-24 16:36:33,349 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Rslt: (ome.model.meta.Experimenter:Id_0, ome.model.meta.ExperimenterGroup:Id_0, (0, 1), ... 4 more)
2015-03-24 16:36:33,351 INFO [ org.perf4j.TimingLogger] (Server-120) start[1427214993337] time[13] tag[omero.call.success.ome.logic.AdminImpl.getEventContext]
2015-03-24 16:36:33,351 INFO [ ome.services.util.ServiceHandler] (Server-120) Rslt: ome.system.SimpleEventContext at 41e156f6
2015-03-24 16:36:33,353 INFO [ omero.cmd.SessionI] (Server-119) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/e83a7dc9-30c6-4bd3-a23c-735adfe52b02omero.api.ISession(omero.api._ISessionTie at e1943dae)
2015-03-24 16:36:33,354 INFO [ ome.services.util.ServiceHandler] (Server-120) Meth: interface ome.api.ISession.getSession
2015-03-24 16:36:33,354 INFO [ ome.services.util.ServiceHandler] (Server-120) Args: [c8e1208f-31bc-405c-90d0-b580515a00e8]
2015-03-24 16:36:33,354 INFO [ org.perf4j.TimingLogger] (Server-120) start[1427214993354] time[0] tag[omero.call.success.ome.services.sessions.SessionBean.getSession]
2015-03-24 16:36:33,354 INFO [ ome.services.util.ServiceHandler] (Server-120) Rslt: ome.model.meta.Session:Id_2277
2015-03-24 16:36:33,373 INFO [ ome.services.util.ServiceHandler] (Server-119) Meth: interface ome.api.IAdmin.getEventContext
2015-03-24 16:36:33,373 INFO [ ome.services.util.ServiceHandler] (Server-119) Args: ()
2015-03-24 16:36:33,375 INFO [ ome.security.basic.EventHandler] (Server-119) Auth: user=0,group=0,event=null(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:33,375 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[c8e1208f-31bc-405c-90d0-b580515a00e8]
2015-03-24 16:36:33,375 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Args: [null, InternalSF at 727982057]
2015-03-24 16:36:33,377 INFO [ ome.security.basic.EventHandler] (3-thread-4) Auth: user=0,group=0,event=null(Sessions),sess=afe0ab3d-4f54-47c2-91e8-487d111d9f63
2015-03-24 16:36:33,383 INFO [ org.perf4j.TimingLogger] (3-thread-4) start[1427214993375] time[8] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2015-03-24 16:36:33,383 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Rslt: (ome.model.meta.Experimenter:Id_0, ome.model.meta.ExperimenterGroup:Id_0, (0, 1), ... 4 more)
2015-03-24 16:36:33,385 INFO [ org.perf4j.TimingLogger] (Server-119) start[1427214993373] time[12] tag[omero.call.success.ome.logic.AdminImpl.getEventContext]
2015-03-24 16:36:33,385 INFO [ ome.services.util.ServiceHandler] (Server-119) Rslt: ome.system.SimpleEventContext at 4db48c8e
2015-03-24 16:36:44,795 INFO [ ome.services.blitz.fire.SessionManagerI] (Server-118) Found session locally: c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:44,796 INFO [ ome.services.blitz.fire.SessionManagerI] (Server-118) Rejoining session ServiceFactoryI(session-bb1aafd1-814b-4767-92f7-876c3323d52c/c8e1208f-31bc-405c-90d0-b580515a00e8) (agent=OMERO.importer)
2015-03-24 16:36:44,838 INFO [ omero.cmd.SessionI] (Server-120) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/bb1aafd1-814b-4767-92f7-876c3323d52comero.api.IConfig(omero.api._IConfigTie at 689e925)
2015-03-24 16:36:44,847 INFO [ ome.services.util.ServiceHandler] (Server-119) Meth: interface ome.api.IConfig.getConfigValue
2015-03-24 16:36:44,847 INFO [ ome.services.util.ServiceHandler] (Server-119) Args: [omero.router.insecure]
2015-03-24 16:36:44,859 INFO [ ome.security.basic.EventHandler] (Server-119) Auth: user=0,group=0,event=267838(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:44,863 INFO [ org.perf4j.TimingLogger] (Server-119) start[1427215004847] time[15] tag[omero.call.success.ome.logic.ConfigImpl.getConfigValue]
2015-03-24 16:36:44,863 INFO [ ome.services.util.ServiceHandler] (Server-119) Rslt: OMERO.Glacier2/router:tcp -p 4063 -h @omero.host@
2015-03-24 16:36:44,914 INFO [ ome.services.blitz.fire.SessionManagerI] (Server-120) Found session locally: c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:44,915 INFO [ ome.services.blitz.fire.SessionManagerI] (Server-120) Rejoining session ServiceFactoryI(session-c76ce4fb-c045-4f0d-b2d3-801a1c102f5e/c8e1208f-31bc-405c-90d0-b580515a00e8) (agent=OMERO.importer;secure=false)
2015-03-24 16:36:44,924 INFO [ omero.cmd.SessionI] (Server-118) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.IAdmin(omero.api._IAdminTie at fa8d6b50)
2015-03-24 16:36:44,951 INFO [ omero.cmd.SessionI] (Server-120) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.IQuery(omero.api._IQueryTie at 23c46328)
2015-03-24 16:36:44,961 INFO [ ome.services.util.ServiceHandler] (Server-119) Meth: interface ome.api.IAdmin.getEventContext
2015-03-24 16:36:44,961 INFO [ ome.services.util.ServiceHandler] (Server-119) Args: ()
2015-03-24 16:36:44,964 INFO [ ome.security.basic.EventHandler] (Server-119) Auth: user=0,group=0,event=null(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:44,964 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[c8e1208f-31bc-405c-90d0-b580515a00e8]
2015-03-24 16:36:44,964 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Args: [null, InternalSF at 727982057]
2015-03-24 16:36:44,966 INFO [ ome.security.basic.EventHandler] (3-thread-4) Auth: user=0,group=0,event=null(Sessions),sess=afe0ab3d-4f54-47c2-91e8-487d111d9f63
2015-03-24 16:36:44,973 INFO [ org.perf4j.TimingLogger] (3-thread-4) start[1427215004964] time[8] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2015-03-24 16:36:44,973 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Rslt: (ome.model.meta.Experimenter:Id_0, ome.model.meta.ExperimenterGroup:Id_0, (0, 1), ... 4 more)
2015-03-24 16:36:44,974 INFO [ org.perf4j.TimingLogger] (Server-119) start[1427215004961] time[12] tag[omero.call.success.ome.logic.AdminImpl.getEventContext]
2015-03-24 16:36:44,974 INFO [ ome.services.util.ServiceHandler] (Server-119) Rslt: ome.system.SimpleEventContext at 76a0b14e
2015-03-24 16:36:44,980 INFO [ omero.cmd.SessionI] (Server-118) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.IUpdate(omero.api._IUpdateTie at bb472b3d)
2015-03-24 16:36:44,987 INFO [ omero.cmd.SessionI] (Server-120) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/15dcc402-d9b6-4aa7-8a12-548b098a6ba0omero.api.RawFileStore(omero.api._RawFileStoreTie at 30c6d31d)
2015-03-24 16:36:44,997 INFO [ omero.cmd.SessionI] (Server-119) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/38f00ae9-69e7-4111-82ef-fe2868df5aadomero.api.RawPixelsStore(omero.api._RawPixelsStoreTie at e8aef913)
2015-03-24 16:36:45,022 INFO [ omero.cmd.SessionI] (Server-118) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/e7ae743c-890a-43e5-b094-c9b8cf07fd66omero.api.ThumbnailStore(omero.api._ThumbnailStoreTie at f259179d)
2015-03-24 16:36:45,034 INFO [ omero.cmd.SessionI] (Server-120) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.IRepositoryInfo(omero.api._IRepositoryInfoTie at c0527c3)
2015-03-24 16:36:45,040 INFO [ omero.cmd.SessionI] (Server-119) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.IContainer(omero.api._IContainerTie at c84842c0)
2015-03-24 16:36:45,051 INFO [ omero.cmd.SessionI] (Server-118) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.IRenderingSettings(omero.api._IRenderingSettingsTie at eaf83fea)
2015-03-24 16:36:45,065 INFO [ omero.cmd.SessionI] (Server-120) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.MetadataStore(omero.api._MetadataStoreTie at e921bc92)
2015-03-24 16:36:45,106 INFO [ omero.cmd.SessionI] (Server-118) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.IConfig(omero.api._IConfigTie at cf19d992)
2015-03-24 16:36:45,107 INFO [ ome.services.util.ServiceHandler] (Server-120) Meth: interface ome.api.IConfig.getVersion
2015-03-24 16:36:45,107 INFO [ ome.services.util.ServiceHandler] (Server-120) Args: ()
2015-03-24 16:36:45,119 INFO [ ome.security.basic.EventHandler] (Server-120) Auth: user=0,group=0,event=267839(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:45,122 INFO [ org.perf4j.TimingLogger] (Server-120) start[1427215005107] time[15] tag[omero.call.success.ome.logic.ConfigImpl.getVersion]
2015-03-24 16:36:45,122 INFO [ ome.services.util.ServiceHandler] (Server-120) Rslt: 5.1.0
2015-03-24 16:36:45,147 INFO [ omero.cmd.SessionI] (Server-119) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.grid.SharedResources(omero.grid._SharedResourcesTie at d8a9903e)
2015-03-24 16:36:45,153 INFO [ ome.services.util.ServiceHandler] (Server-118) Executor.doWork -- ome.services.blitz.impl.SharedResourcesI.acquireRepositories[]
2015-03-24 16:36:45,153 INFO [ ome.services.util.ServiceHandler] (Server-118) Args: [null, InternalSF at 727982057]
2015-03-24 16:36:45,155 INFO [ ome.security.basic.EventHandler] (Server-118) Auth: user=0,group=0,event=null(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:45,160 INFO [ org.perf4j.TimingLogger] (Server-118) start[1427215005153] time[7] tag[omero.call.success.ome.services.blitz.impl.SharedResourcesI$1.doWork]
2015-03-24 16:36:45,160 INFO [ ome.services.util.ServiceHandler] (Server-118) Rslt: (ome.model.core.OriginalFile:Id_2, ome.model.core.OriginalFile:Id_1, ome.model.core.OriginalFile:Id_3)
2015-03-24 16:36:45,162 INFO [ ome.services.blitz.fire.Registry] (Server-118) Found 3 repo(s) : [InternalRepository-ScriptRepo -t -e 1.1:tcp -h 10.3.2.140 -p 45326, InternalRepository-06cb5cdd-daba-49d5-8156-25d85ef88e50 -t -e 1.1:tcp -h 10.3.2.140 -p 45326, InternalRepository-2ddacd43-f4bf-4d3e-a2b7-01a03a5fe11e -t -e 1.1:tcp -h 10.3.2.140 -p 45326]
2015-03-24 16:36:45,198 INFO [ ome.services.util.ServiceHandler] (Server-120) Meth: interface ome.api.IQuery.get
2015-03-24 16:36:45,198 INFO [ ome.services.util.ServiceHandler] (Server-120) Args: [class ome.model.containers.Dataset, 1]
2015-03-24 16:36:45,199 INFO [ ome.security.basic.BasicEventContext] (Server-120) cctx: group=-1
2015-03-24 16:36:45,202 INFO [ ome.security.basic.EventHandler] (Server-120) Auth: user=0,group=-1,event=null(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:45,205 INFO [ org.perf4j.TimingLogger] (Server-120) start[1427215005198] time[7] tag[omero.call.success.ome.logic.QueryImpl.get]
2015-03-24 16:36:45,205 INFO [ ome.services.util.ServiceHandler] (Server-120) Rslt: ome.model.containers.Dataset:Id_1
2015-03-24 16:36:45,216 INFO [ ome.services.util.ServiceHandler] (Server-119) Meth: interface ome.api.StatefulServiceInterface.close
2015-03-24 16:36:45,216 INFO [ ome.services.util.ServiceHandler] (Server-119) Args: ()
2015-03-24 16:36:45,227 INFO [ ome.security.basic.EventHandler] (Server-119) Auth: user=0,group=0,event=267840(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:45,230 INFO [ org.perf4j.TimingLogger] (Server-119) start[1427215005216] time[14] tag[omero.call.success.ome.services.RawFileBean.close]
2015-03-24 16:36:45,230 INFO [ ome.services.util.ServiceHandler] (Server-119) Rslt: null
2015-03-24 16:36:45,230 INFO [ ome.services.util.ServiceHandler] (Server-119) Cleanup: ome.services.RawFileBean at 3ba12861
2015-03-24 16:36:45,231 INFO [ omero.cmd.SessionI] (Server-119) Unregistered servant:c8e1208f-31bc-405c-90d0-b580515a00e8/15dcc402-d9b6-4aa7-8a12-548b098a6ba0omero.api.RawFileStore(omero.api._RawFileStoreTie at 30c6d31d)
2015-03-24 16:36:45,233 INFO [ ome.services.util.ServiceHandler] (Server-118) Meth: interface ome.api.StatefulServiceInterface.close
2015-03-24 16:36:45,233 INFO [ ome.services.util.ServiceHandler] (Server-118) Args: ()
2015-03-24 16:36:45,243 INFO [ ome.security.basic.EventHandler] (Server-118) Auth: user=0,group=0,event=267841(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:45,245 INFO [ org.perf4j.TimingLogger] (Server-118) start[1427215005233] time[11] tag[omero.call.success.ome.services.RawPixelsBean.close]
2015-03-24 16:36:45,245 INFO [ ome.services.util.ServiceHandler] (Server-118) Rslt: null
2015-03-24 16:36:45,245 INFO [ ome.services.util.ServiceHandler] (Server-118) Cleanup: ome.services.RawPixelsBean at 3e88298e
2015-03-24 16:36:45,245 INFO [ omero.cmd.SessionI] (Server-118) Unregistered servant:c8e1208f-31bc-405c-90d0-b580515a00e8/38f00ae9-69e7-4111-82ef-fe2868df5aadomero.api.RawPixelsStore(omero.api._RawPixelsStoreTie at e8aef913)
2015-03-24 16:36:45,247 INFO [ ome.services.util.ServiceHandler] (Server-120) Meth: interface ome.api.StatefulServiceInterface.close
2015-03-24 16:36:45,247 INFO [ ome.services.util.ServiceHandler] (Server-120) Args: ()
2015-03-24 16:36:45,249 INFO [ ome.security.basic.EventHandler] (Server-120) Auth: user=0,group=0,event=null(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:45,250 INFO [ org.perf4j.TimingLogger] (Server-120) start[1427215005247] time[2] tag[omero.call.success.ome.services.ThumbnailBean.close]
2015-03-24 16:36:45,250 INFO [ ome.services.util.ServiceHandler] (Server-120) Rslt: null
2015-03-24 16:36:45,251 INFO [ ome.services.util.ServiceHandler] (Server-120) Cleanup: ome.services.ThumbnailBean at d118718
2015-03-24 16:36:45,251 INFO [ omero.cmd.SessionI] (Server-120) Unregistered servant:c8e1208f-31bc-405c-90d0-b580515a00e8/e7ae743c-890a-43e5-b094-c9b8cf07fd66omero.api.ThumbnailStore(omero.api._ThumbnailStoreTie at f259179d)
2015-03-24 16:36:45,252 INFO [ omero.cmd.SessionI] (Server-119) Unregistered servant:c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.MetadataStore(omero.api._MetadataStoreTie at e921bc92)
2015-03-24 16:36:45,257 INFO [ ome.services.util.ServiceHandler] (Server-120) Meth: interface ome.api.IAdmin.getEventContext
2015-03-24 16:36:45,257 INFO [ ome.services.util.ServiceHandler] (Server-120) Args: ()
2015-03-24 16:36:45,259 INFO [ ome.security.basic.BasicEventContext] (Server-120) cctx: group=0
2015-03-24 16:36:45,259 INFO [ ome.security.basic.EventHandler] (Server-120) Auth: user=0,group=0,event=null(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:45,259 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[c8e1208f-31bc-405c-90d0-b580515a00e8]
2015-03-24 16:36:45,259 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Args: [null, InternalSF at 727982057]
2015-03-24 16:36:45,261 INFO [ ome.security.basic.EventHandler] (3-thread-4) Auth: user=0,group=0,event=null(Sessions),sess=afe0ab3d-4f54-47c2-91e8-487d111d9f63
2015-03-24 16:36:45,268 INFO [ org.perf4j.TimingLogger] (3-thread-4) start[1427215005259] time[8] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2015-03-24 16:36:45,268 INFO [ ome.services.util.ServiceHandler] (3-thread-4) Rslt: (ome.model.meta.Experimenter:Id_0, ome.model.meta.ExperimenterGroup:Id_0, (0, 1), ... 4 more)
2015-03-24 16:36:45,269 INFO [ org.perf4j.TimingLogger] (Server-120) start[1427215005257] time[12] tag[omero.call.success.ome.logic.AdminImpl.getEventContext]
2015-03-24 16:36:45,269 INFO [ ome.services.util.ServiceHandler] (Server-120) Rslt: ome.system.SimpleEventContext at 4e4ea381
2015-03-24 16:36:45,272 INFO [ omero.cmd.SessionI] (Server-119) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/47d7d8a0-1300-43b3-a0eb-6293bd68e1c7omero.api.RawFileStore(omero.api._RawFileStoreTie at ec065d96)
2015-03-24 16:36:45,274 INFO [ omero.cmd.SessionI] (Server-120) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/8b667ac5-f409-43c2-80f2-c3442d212bdcomero.api.RawPixelsStore(omero.api._RawPixelsStoreTie at fb20a57f)
2015-03-24 16:36:45,276 INFO [ omero.cmd.SessionI] (Server-118) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/0fe6d496-b144-4649-a6c4-e8b127487b92omero.api.ThumbnailStore(omero.api._ThumbnailStoreTie at c3b087e7)
2015-03-24 16:36:45,279 INFO [ omero.cmd.SessionI] (Server-119) Added servant to adapter: c8e1208f-31bc-405c-90d0-b580515a00e8/c76ce4fb-c045-4f0d-b2d3-801a1c102f5eomero.api.MetadataStore(omero.api._MetadataStoreTie at f9bba179)
2015-03-24 16:36:45,297 INFO [ ome.services.util.ServiceHandler] (Server-118) Meth: interface ome.api.StatefulServiceInterface.close
2015-03-24 16:36:45,297 INFO [ ome.services.util.ServiceHandler] (Server-118) Args: ()
2015-03-24 16:36:45,299 INFO [ ome.security.basic.BasicEventContext] (Server-118) cctx: group=0
2015-03-24 16:36:45,309 INFO [ ome.security.basic.EventHandler] (Server-118) Auth: user=0,group=0,event=267842(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:45,310 INFO [ org.perf4j.TimingLogger] (Server-118) start[1427215005297] time[13] tag[omero.call.success.ome.services.RawFileBean.close]
2015-03-24 16:36:45,311 INFO [ ome.services.util.ServiceHandler] (Server-118) Rslt: null
2015-03-24 16:36:45,311 INFO [ ome.services.util.ServiceHandler] (Server-118) Cleanup: ome.services.RawFileBean at 1e52ef31
2015-03-24 16:36:45,311 INFO [ omero.cmd.SessionI] (Server-118) Unregistered servant:c8e1208f-31bc-405c-90d0-b580515a00e8/47d7d8a0-1300-43b3-a0eb-6293bd68e1c7omero.api.RawFileStore(omero.api._RawFileStoreTie at ec065d96)
2015-03-24 16:36:45,312 INFO [ ome.services.util.ServiceHandler] (Server-119) Meth: interface ome.api.StatefulServiceInterface.close
2015-03-24 16:36:45,312 INFO [ ome.services.util.ServiceHandler] (Server-119) Args: ()
2015-03-24 16:36:45,314 INFO [ ome.security.basic.BasicEventContext] (Server-119) cctx: group=0
2015-03-24 16:36:45,322 INFO [ ome.security.basic.EventHandler] (Server-119) Auth: user=0,group=0,event=267843(User),sess=c8e1208f-31bc-405c-90d0-b580515a00e8
2015-03-24 16:36:45,324 INFO [ org.perf4j.TimingLogger] (Server-119) start[1427215005312] time[12] tag[omero.call.success.ome.services.RawPixelsBean.close]
> On 24 Mar 2015, at 14:01, Sebastien Besson (Staff) <s.besson at dundee.ac.uk> wrote:
>
> Hi José,
>
> have you tried following the suggestion from the troubleshooting section of the
> documentation
> http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/troubleshooting.html#server-fails-to-start <http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/troubleshooting.html#server-fails-to-start>
> If not, can you try and let us know if that clears the problem in master.err?
>
> Best regards,
> Sebastien
>
>> On 24 Mar 2015, at 13:50, José Salavert Torres <josator at ebi.ac.uk <mailto:josator at ebi.ac.uk>> wrote:
>>
>> I did that already with:
>>
>> omero admin stop
>> omero admin start
>>
>> and the problem persists.
>>
>> How can this lock be released?
>>
>>> On 24 Mar 2015, at 13:43, Josh Moore <josh at glencoesoftware.com <mailto:josh at glencoesoftware.com>> wrote:
>>>
>>> On Tue, Mar 24, 2015 at 1:36 PM, José Salavert Torres <josator at ebi.ac.uk <mailto:josator at ebi.ac.uk>> wrote:
>>>> I have extracted with grep the error messages:
>>>
>>> Thanks, José. The most related error message I see is from master.err:
>>>
>>> !! 03/23/15 11:23:45.482 OMERO.IceStorm: error: ServiceManager:
>>> exception while starting service OMERO.IceStorm:
>>> FileUtil.cpp:385: IceUtil::FileLockedException:
>>> could not lock file:
>>> `/net/isilonP/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/var/master/servers/OMERO.IceStorm/dbs/OMERO.IceStorm/__Freeze/lock'
>>> syscall exception: Resource temporarily unavailable
>>>
>>> When was the last time the server was restarted? If before that time,
>>> can it be restarted and then master.err checked for the same problem?
>>>
>>> Cheers,
>>> ~Josh.
>>>
>>>
>>>
>>>> On 24 Mar 2015, at 11:24, Josh Moore <josh at glencoesoftware.com <mailto:josh at glencoesoftware.com>> wrote:
>>>>
>>>> Hi José,
>>>>
>>>>
>>>> On Tue, Mar 24, 2015 at 10:59 AM, José Salavert Torres
>>>> <josator at ebi.ac.uk <mailto:josator at ebi.ac.uk>> wrote:
>>>>
>>>> Sorry, I can not execute the second command, I do not have root permissions
>>>> on the OMERO machine.
>>>>
>>>>
>>>> Hmmm....do you have access to the server logs? Can you put us in
>>>> contact with your server administrator?
>>>>
>>>> Thanks,
>>>> ~Josh
>>>>
>>>> (I had to build and manually install every dependency).
>>>>
>>>> omero admin diagnostics
>>>>
>>>> ================================================================================
>>>> OMERO Diagnostics 5.1.0-m2-ice35-SNAPSHOT
>>>> ================================================================================
>>>>
>>>> Commands: java -version 1.6.0 (/usr/bin/java)
>>>> Commands: python -V 2.6.6
>>>> (/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin/python -- 2
>>>> others)
>>>> Commands: icegridnode --version 3.5.1
>>>> (/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridnode)
>>>> Commands: icegridadmin --version 3.5.1
>>>> (/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin/icegridadmin)
>>>> Commands: psql --version 8.4.20 (/usr/bin/psql)
>>>>
>>>> Server: icegridnode running
>>>> Server: Blitz-0 active (pid = 4104, enabled)
>>>> Server: DropBox active (pid = 4116, enabled)
>>>> Server: FileServer active (pid = 4123, enabled)
>>>> Server: Indexer-0 active (pid = 4125, enabled)
>>>> Server: MonitorServer active (pid = 4124, enabled)
>>>> Server: OMERO.Glacier2 active (pid = 4126, enabled)
>>>> Server: OMERO.IceStorm inactive (disabled)
>>>> Server: PixelData-0 active (pid = 4129, enabled)
>>>> Server: Processor-0 active (pid = 4127, enabled)
>>>> Server: Tables-0 inactive (disabled)
>>>> Server: TestDropBox inactive (enabled)
>>>>
>>>> Log dir:
>>>> /nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/var/log
>>>> exists
>>>>
>>>> Log files: Blitz-0.log 17.0 MB errors=1
>>>> warnings=912
>>>> Log files: Blitz-0.log.1 524.0 MB errors=65
>>>> warnings=9855
>>>> Log files: Blitz-0.log.2 524.0 MB errors=3900
>>>> warnings=6595
>>>> Log files: DropBox.log 41.0 KB errors=20
>>>> warnings=19
>>>> Log files: FileServer.log 7.0 KB errors=2
>>>> warnings=0
>>>> Log files: Indexer-0.log 2.0 MB errors=162
>>>> warnings=590
>>>> Log files: MonitorServer.log 20.0 KB errors=3
>>>> warnings=0
>>>> Log files: OMEROweb.log 1.0 MB errors=316
>>>> warnings=294
>>>> Log files: OMEROweb_request.log 176.0 KB errors=205
>>>> warnings=290
>>>> Log files: PixelData-0.log 419.0 KB errors=23
>>>> warnings=290
>>>> Log files: Processor-0.log 109.0 KB errors=46
>>>> warnings=30
>>>> Log files: Tables-0.log n/a
>>>> Log files: TestDropBox.log n/a
>>>> Log files: master.err 78.0 KB errors=53
>>>> warnings=53
>>>> Log files: master.out 0.0 KB errors=1
>>>> warnings=0
>>>> Log files: Total size 1070.65 MB
>>>>
>>>>
>>>> Environment:OMERO_HOME=(unset)
>>>> Environment:OMERO_NODE=(unset)
>>>> Environment:OMERO_MASTER=(unset)
>>>> Environment:OMERO_TEMPDIR=(unset)
>>>> Environment:PATH=/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/bin:/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/bin:/nfs/public/rw/pdbe/mol2cell/software/bin:/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/bin:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/bin:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/bin:/usr/lib64/ccache:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/net/isilonP/public/rw/homes/pdb_em/bin
>>>> Environment:PYTHONPATH=/nfs/public/rw/pdbe/mol2cell/omero/development/openmicroscopy/dist/lib/python:/nfs/public/rw/pdbe/mol2cell/software/python2.6-virt-env/lib/python2.6:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/python::/net/isilonP/public/rw/homes/pdb_em/python-2.6-libraries
>>>> Environment:ICE_HOME=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1
>>>> Environment:LD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/IMOD/IMOD/lib:/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib64:/nfs/public/rw/pdbe/mol2cell/software/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared/lib:
>>>> Environment:DYLD_LIBRARY_PATH=/nfs/public/rw/pdbe/mol2cell/software/Ice-3.5.1/lib:
>>>>
>>>> OMERO SSL port:4064
>>>> OMERO TCP port:4063
>>>> OMERO data
>>>> dir:'/nfs/public/rw/pdbe/mol2cell/omero/development/var/OMERO.data' Exists?
>>>> True Is writable? True
>>>> OMERO temp dir:'/net/isilonP/public/rw/homes/pdb_em/omero/tmp' Exists? True
>>>> Is writable? True (Size: 0)
>>>>
>>>> JVM settings: Blitz -Xmx602m -XX:MaxPermSize=512m
>>>> JVM settings: Indexer -Xmx401m -XX:MaxPermSize=512m
>>>> JVM settings: Pixeldata -Xmx602m -XX:MaxPermSize=512m
>>>> JVM settings: Repository -Xmx401m -XX:MaxPermSize=512m
>>>>
>>>> OMERO.web status... [RUNNING] (PID 4375)
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 23 Mar 2015, at 18:54, Josh Moore <josh at glencoesoftware.com <mailto:josh at glencoesoftware.com>> wrote:
>>>>
>>>> Hi José,
>>>>
>>>> On Mon, Mar 23, 2015 at 2:11 PM, José Salavert Torres <josator at ebi.ac.uk <mailto:josator at ebi.ac.uk>>
>>>> wrote:
>>>>
>>>> Dear OMERO users:
>>>>
>>>> I was able to do the import before but now without changing configuration or
>>>> anything it fails from any machine (even localhost). However Romero insight
>>>> is working properly. Can you help me?:
>>>>
>>>> ...
>>>>
>>>> 2015-03-23 10:40:43,444 2219 [ main] ERROR
>>>> ome.formats.importer.ImportLibrary - Error on import
>>>> java.lang.RuntimeException: Cannot exclusively use the managed repository.
>>>> at
>>>> ome.formats.importer.ImportLibrary.checkManagedRepo(ImportLibrary.java:709)
>>>> ~[blitz.jar:na]
>>>> at
>>>> ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:316)
>>>> ~[blitz.jar:na]
>>>> at
>>>> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:465)
>>>> ~[blitz.jar:na]
>>>> at
>>>> ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271)
>>>> ~[blitz.jar:na]
>>>> at
>>>> ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216)
>>>> [blitz.jar:na]
>>>> at
>>>> ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:752)
>>>> [blitz.jar:na]
>>>> 2015-03-23 10:40:43,444 2219 [ main] INFO
>>>> ome.formats.importer.ImportLibrary - Exiting on error
>>>>
>>>>
>>>> This looks like there is some server error. Could you provide use the output
>>>> of:
>>>>
>>>> $ bin/omero admin diagnostics
>>>>
>>>> as well as:
>>>>
>>>>
>>>> $ bin/omero -s root at localhost fs repos
>>>>
>>>> e.g.
>>>>
>>>> # | Id | UUID | Type | Path
>>>> ---+-------+--------------------------------------+---------+-------------------------------------------------------------------
>>>> 0 | 17 | ce1e2766-089f-4555-a52a-f75746fd44da | Public |
>>>> /repositories/OMERO-5.0-latest-deploy
>>>> 1 | 18 | ScriptRepo | Script |
>>>> /opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/scripts
>>>> 2 | 10901 | a5a2b4b3-d146-4ccc-98fa-7353a1ba023b | Managed |
>>>> /repositories/OMERO-5.1-merge-deploy/ManagedRepository
>>>> 3 | 18651 | 34b38044-0ff6-4019-8f97-4e0093f5a3c3 | Public |
>>>> /repositories/OMERO-5.0-latest-deploy
>>>> 4 | 18701 | 640d985e-0ba5-47a6-bacb-42b7cf60354b | Public |
>>>> /repositories/OMERO-5.1-merge-deploy
>>>> (5 rows)
>>>>
>>>> Cheers,
>>>> ~Josh
>>>> _______________________________________________
>>>> ome-users mailing list
>>>> ome-users at lists.openmicroscopy.org.uk <mailto:ome-users at lists.openmicroscopy.org.uk>
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>
>>>>
>>>>
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>>>>
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>>>>
>>>>
>>>>
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>>>>
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>
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