Open Microscopy Environment

Dear all,

After successfully running omero server 4.2.2 for a few months, I upgraded to 4.3.0 following the guidelines provided on omero website and all run smoothly. Old data are working perfectly in OMERO.insight but importing new data (all clients upgraded as well of course), the previews and thumbnails are not geenrated. insight show a clock in the place of the thumbnail and double clicking on it pops the message "Cannot start the Rendering Engine. Image not ready. Please try again later." This message stays days after import. I then upgraded to 4.3.1 without more success. The log of importer does not contain any error (attached and named importer.log). On server side, there is some error in Blitz-0.log (in 3 parts to go around the size limitation). I attach the full log and paste below some pieces that looks to me related. If someone could tell me a few suggestions to fix that issue, it would be very grateful.
Thank you very much in advance

Best regards

Jacques

================================================

2011-07-14 22:14:34,181 INFO [ome.services.sessions.state.SessionCache] (3-thread-5) Synchronizing session cache. Count = 7
2011-07-14 22:14:34,181 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload(5c32f8cc-1002-4c8d-b72a-c4694d549dd5)
2011-07-14 22:14:34,181 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Args: [null, InternalSF@1426511082]
2011-07-14 22:14:34,185 INFO [ ome.security.basic.EventHandler] (3-thread-5) Auth: user=0,group=0,event=null(Sessions),sess=5c32f8cc-1002-4c8d-b72a-c4694d549dd5
2011-07-14 22:14:34,194 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1310674474181] time[13] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2011-07-14 22:14:34,194 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Rslt: (ome.model.meta.Experimenter:Id_0, ome.model.meta.ExperimenterGroup:Id_0, [0, 1], ... 4 more)
2011-07-14 22:14:34,194 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload(94198245-3809-471f-b613-7d787b4aaa43)
2011-07-14 22:14:34,194 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Args: [null, InternalSF@1426511082]
2011-07-14 22:14:34,194 INFO [ ome.security.basic.EventHandler] (3-thread-5) Auth: user=0,group=0,event=null(Sessions),sess=5c32f8cc-1002-4c8d-b72a-c4694d549dd5
2011-07-14 22:14:34,199 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1310674474194] time[5] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2011-07-14 22:14:34,199 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Rslt: (ome.model.meta.Experimenter:Id_1, ome.model.meta.ExperimenterGroup:Id_2, [2], ... 4 more)
2011-07-14 22:14:34,199 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload(d72ca382-9130-4847-830d-9799904901d2)
2011-07-14 22:14:34,199 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Args: [null, InternalSF@1426511082]
2011-07-14 22:14:34,199 INFO [ ome.security.basic.EventHandler] (3-thread-5) Auth: user=0,group=0,event=null(Sessions),sess=5c32f8cc-1002-4c8d-b72a-c4694d549dd5
2011-07-14 22:14:34,203 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1310674474199] time[4] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2011-07-14 22:14:34,203 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Rslt: (ome.model.meta.Experimenter:Id_0, ome.model.meta.ExperimenterGroup:Id_0, [0, 1], ... 4 more)
2011-07-14 22:14:34,204 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload(384812b5-21d4-450a-90b6-21e797a1ad4b)
2011-07-14 22:14:34,204 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Args: [null, InternalSF@1426511082]
2011-07-14 22:14:34,204 INFO [ ome.security.basic.EventHandler] (3-thread-5) Auth: user=0,group=0,event=null(Sessions),sess=5c32f8cc-1002-4c8d-b72a-c4694d549dd5
2011-07-14 22:14:34,208 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1310674474204] time[4] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2011-07-14 22:14:34,208 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Rslt: (ome.model.meta.Experimenter:Id_52, ome.model.meta.ExperimenterGroup:Id_3, [1, 3, 53], ... 4 more)
2011-07-14 22:14:34,209 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload(1d25ed71-3a8f-460c-b401-0e2d6bac5890)
2011-07-14 22:14:34,209 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Args: [null, InternalSF@1426511082]
2011-07-14 22:14:34,209 INFO [ ome.security.basic.EventHandler] (3-thread-5) Auth: user=0,group=0,event=null(Sessions),sess=5c32f8cc-1002-4c8d-b72a-c4694d549dd5
2011-07-14 22:14:34,213 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1310674474209] time[4] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2011-07-14 22:14:34,213 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Rslt: (ome.model.meta.Experimenter:Id_52, ome.model.meta.ExperimenterGroup:Id_3, [1, 3, 53], ... 4 more)
2011-07-14 22:14:34,213 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload(acb1600a-b23c-4c0c-84a2-4de094d06938)
2011-07-14 22:14:34,213 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Args: [null, InternalSF@1426511082]
2011-07-14 22:14:34,214 INFO [ ome.security.basic.EventHandler] (3-thread-5) Auth: user=0,group=0,event=null(Sessions),sess=5c32f8cc-1002-4c8d-b72a-c4694d549dd5
2011-07-14 22:14:34,218 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1310674474213] time[5] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2011-07-14 22:14:34,218 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Rslt: (ome.model.meta.Experimenter:Id_52, ome.model.meta.ExperimenterGroup:Id_3, [1, 3, 53], ... 4 more)
2011-07-14 22:14:34,218 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload(83ff0ccc-eef8-44dd-9f25-f76811c927a6)
2011-07-14 22:14:34,218 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Args: [null, InternalSF@1426511082]
2011-07-14 22:14:34,219 INFO [ ome.security.basic.EventHandler] (3-thread-5) Auth: user=0,group=0,event=null(Sessions),sess=5c32f8cc-1002-4c8d-b72a-c4694d549dd5
2011-07-14 22:14:34,223 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1310674474218] time[5] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2011-07-14 22:14:34,223 INFO [ ome.services.util.ServiceHandler] (3-thread-5) Rslt: (ome.model.meta.Experimenter:Id_0, ome.model.meta.ExperimenterGroup:Id_0, [0, 1], ... 4 more)
2011-07-14 22:14:34,223 INFO [ org.perf4j.TimingLogger] (3-thread-5) start[1310674474181] time[42] tag[omero.sessions.synchronization]
2011-07-14 22:14:34,223 INFO [ome.services.sessions.state.SessionCache] (3-thread-5) Synchronization took 42 ms.
2011-07-14 22:15:00,019 INFO [ ome.services.blitz.fire.SessionManagerI] (3-thread-3) Performing requestHeartbeats
2011-07-14 22:15:07,415 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Session already removed. Cleaning up blitz state.
2011-07-14 22:15:07,415 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-4) Session already removed. Cleaning up blitz state.
2011-07-14 22:15:07,415 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) doDestroy(ServiceFactoryI(session-e0d49efc-0930-4c8e-842d-10cd307e2c8a/acb1600a-b23c-4c0c-84a2-4de094d06938))
2011-07-14 22:15:07,415 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-9) Session already removed. Cleaning up blitz state.
2011-07-14 22:15:07,415 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-4) doDestroy(ServiceFactoryI(session-d4d1cfed-e7ff-43a5-ba9c-05f8a0b4821f/acb1600a-b23c-4c0c-84a2-4de094d06938))
2011-07-14 22:15:07,415 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-9) doDestroy(ServiceFactoryI(session-8c6414b7-3966-48a8-b47e-175fd0acc37a/acb1600a-b23c-4c0c-84a2-4de094d06938))
2011-07-14 22:15:07,415 INFO [ ome.services.blitz.impl.ServiceFactoryI] (.Server-10) Session already removed. Cleaning up blitz state.
2011-07-14 22:15:07,416 INFO [ ome.services.blitz.impl.ServiceFactoryI] (.Server-10) doDestroy(ServiceFactoryI(session-b9ef88b0-0c96-49e8-9d78-18e40203566b/acb1600a-b23c-4c0c-84a2-4de094d06938))
2011-07-14 22:15:07,416 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Session already removed. Cleaning up blitz state.
2011-07-14 22:15:07,416 INFO [ ome.services.blitz.impl.ThumbnailStoreI] (l.Server-6) NoSuchElementException: Login is already gone
2011-07-14 22:15:07,416 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) doDestroy(ServiceFactoryI(session-5e1dbb63-0dac-4533-a365-4e45dfe91929/acb1600a-b23c-4c0c-84a2-4de094d06938))
2011-07-14 22:15:07,417 ERROR [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Error destroying servant: 81:14:9f:a5:-7cf50bc9:1312906d072:-7fe2omero.api.ThumbnailStore=ome.services.blitz.impl.ThumbnailStoreI@1abb3cd8
java.lang.RuntimeException: omero.InternalException
serverStackTrace = "java.util.NoSuchElementException
at java.util.LinkedList.remove(LinkedList.java:788)
at java.util.LinkedList.removeLast(LinkedList.java:144)
at ome.security.basic.CurrentDetails.logout(CurrentDetails.java:180)
at ome.security.basic.BasicSecurityWiring.logout(BasicSecurityWiring.java:110)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy78.close(Unknown Source)
at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:227)
at ome.services.blitz.impl.AbstractAmdServant.close(AbstractAmdServant.java:198)
at ome.services.blitz.impl.ServiceFactoryI.doDestroy(ServiceFactoryI.java:790)
at ome.services.blitz.impl.ServiceFactoryI.destroy(ServiceFactoryI.java:703)
at Glacier2._SessionDisp.___destroy(_SessionDisp.java:82)
at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1263)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
"
serverExceptionClass = "java.util.NoSuchElementException"
message = (null)
at ome.services.blitz.impl.AbstractAmdServant$1.ice_exception(AbstractAmdServant.java:191)
at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:255)
at ome.services.blitz.impl.AbstractAmdServant.close(AbstractAmdServant.java:198)
at ome.services.blitz.impl.ServiceFactoryI.doDestroy(ServiceFactoryI.java:790)
at ome.services.blitz.impl.ServiceFactoryI.destroy(ServiceFactoryI.java:703)
at Glacier2._SessionDisp.___destroy(_SessionDisp.java:82)
at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1263)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
Caused by: omero.InternalException
serverStackTrace = "java.util.NoSuchElementException
at java.util.LinkedList.remove(LinkedList.java:788)
at java.util.LinkedList.removeLast(LinkedList.java:144)
at ome.security.basic.CurrentDetails.logout(CurrentDetails.java:180)
at ome.security.basic.BasicSecurityWiring.logout(BasicSecurityWiring.java:110)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy78.close(Unknown Source)
at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:227)
at ome.services.blitz.impl.AbstractAmdServant.close(AbstractAmdServant.java:198)
at ome.services.blitz.impl.ServiceFactoryI.doDestroy(ServiceFactoryI.java:790)
at ome.services.blitz.impl.ServiceFactoryI.destroy(ServiceFactoryI.java:703)
at Glacier2._SessionDisp.___destroy(_SessionDisp.java:82)
at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1263)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
"
serverExceptionClass = "java.util.NoSuchElementException"
message = (null)
at omero.util.IceMapper.handleException(IceMapper.java:1298)
... 12 more
2011-07-14 22:15:07,417 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:acb1600a-b23c-4c0c-84a2-4de094d06938/81:14:9f:a5:-7cf50bc9:1312906d072:-7fe2omero.api.ThumbnailStore(omero.api._ThumbnailStoreTie@1abb3cd8)
2011-07-14 22:15:07,417 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: 81:14:9f:a5:-7cf50bc9:1312906d072:-7fe2omero.api.ThumbnailStore
2011-07-14 22:15:07,417 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:acb1600a-b23c-4c0c-84a2-4de094d06938/d8432c28-85b1-4b6a-98f3-ebb1ad9b3712omero.api.ISession(omero.api._ISessionTie@6c1ad526)
2011-07-14 22:15:07,417 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: d8432c28-85b1-4b6a-98f3-ebb1ad9b3712omero.api.ISession
2011-07-14 22:15:07,418 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:acb1600a-b23c-4c0c-84a2-4de094d06938/d4d1cfed-e7ff-43a5-ba9c-05f8a0b4821fomero.api.IQuery(omero.api._IQueryTie@4d98d6e9)
2011-07-14 22:15:07,418 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: d4d1cfed-e7ff-43a5-ba9c-05f8a0b4821fomero.api.IQuery
2011-07-14 22:15:07,418 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:acb1600a-b23c-4c0c-84a2-4de094d06938/e0d49efc-0930-4c8e-842d-10cd307e2c8aomero.api.ITimeline(omero.api._ITimelineTie@78dcac8e)
2011-07-14 22:15:07,418 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: e0d49efc-0930-4c8e-842d-10cd307e2c8aomero.api.ITimeline
2011-07-14 22:15:07,418 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:acb1600a-b23c-4c0c-84a2-4de094d06938/5e1dbb63-0dac-4533-a365-4e45dfe91929omero.api.IAdmin(omero.api._IAdminTie@303619bf)
2011-07-14 22:15:07,418 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: 5e1dbb63-0dac-4533-a365-4e45dfe91929omero.api.IAdmin
2011-07-14 22:15:07,418 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:acb1600a-b23c-4c0c-84a2-4de094d06938/8c6414b7-3966-48a8-b47e-175fd0acc37aomero.api.IQuery(omero.api._IQueryTie@6596afe6)
2011-07-14 22:15:07,418 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: 8c6414b7-3966-48a8-b47e-175fd0acc37aomero.api.IQuery
2011-07-14 22:15:07,418 INFO [ ome.services.blitz.impl.ThumbnailStoreI] (l.Server-6) NoSuchElementException: Login is already gone
2011-07-14 22:15:07,419 ERROR [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Error destroying servant: 81:14:9f:a5:-7cf50bc9:1312906d072:-7fe4omero.api.ThumbnailStore=ome.services.blitz.impl.ThumbnailStoreI@62f41e09
java.lang.RuntimeException: omero.InternalException
serverStackTrace = "java.util.NoSuchElementException
at java.util.LinkedList.remove(LinkedList.java:788)
at java.util.LinkedList.removeLast(LinkedList.java:144)
at ome.security.basic.CurrentDetails.logout(CurrentDetails.java:180)
at ome.security.basic.BasicSecurityWiring.logout(BasicSecurityWiring.java:110)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy78.close(Unknown Source)
at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:227)
at ome.services.blitz.impl.AbstractAmdServant.close(AbstractAmdServant.java:198)
at ome.services.blitz.impl.ServiceFactoryI.doDestroy(ServiceFactoryI.java:790)
at ome.services.blitz.impl.ServiceFactoryI.destroy(ServiceFactoryI.java:703)
at Glacier2._SessionDisp.___destroy(_SessionDisp.java:82)
at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1263)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
"
serverExceptionClass = "java.util.NoSuchElementException"
message = (null)
at ome.services.blitz.impl.AbstractAmdServant$1.ice_exception(AbstractAmdServant.java:191)
at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:255)
at ome.services.blitz.impl.AbstractAmdServant.close(AbstractAmdServant.java:198)
at ome.services.blitz.impl.ServiceFactoryI.doDestroy(ServiceFactoryI.java:790)
at ome.services.blitz.impl.ServiceFactoryI.destroy(ServiceFactoryI.java:703)
at Glacier2._SessionDisp.___destroy(_SessionDisp.java:82)
at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1263)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
Caused by: omero.InternalException
serverStackTrace = "java.util.NoSuchElementException
at java.util.LinkedList.remove(LinkedList.java:788)
at java.util.LinkedList.removeLast(LinkedList.java:144)
at ome.security.basic.CurrentDetails.logout(CurrentDetails.java:180)
at ome.security.basic.BasicSecurityWiring.logout(BasicSecurityWiring.java:110)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy78.close(Unknown Source)
at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:227)
at ome.services.blitz.impl.AbstractAmdServant.close(AbstractAmdServant.java:198)
at ome.services.blitz.impl.ServiceFactoryI.doDestroy(ServiceFactoryI.java:790)
at ome.services.blitz.impl.ServiceFactoryI.destroy(ServiceFactoryI.java:703)
at Glacier2._SessionDisp.___destroy(_SessionDisp.java:82)
at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1263)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
"
serverExceptionClass = "java.util.NoSuchElementException"
message = (null)
at omero.util.IceMapper.handleException(IceMapper.java:1298)
... 12 more
2011-07-14 22:15:07,419 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:acb1600a-b23c-4c0c-84a2-4de094d06938/81:14:9f:a5:-7cf50bc9:1312906d072:-7fe4omero.api.ThumbnailStore(omero.api._ThumbnailStoreTie@62f41e09)

The third part of Blitz-0.log

Could you send your var/log/PixelData-0.log file as well?

Thanks,
~Josh.

Dear Josh,

here is the file (it also contains entry appeared since).

Thanks for your help

Jacques

This would definitely explain the problem:

Code: Select all


Caused by: ome.conditions.InternalException:  Wrapped Exception: (java.lang.OutOfMemoryError):
GC overhead limit exceeded
2011-07-18 13:56:38,525 ERROR [             org.quartz.core.ErrorLogger] (3-thread-3) Job (DEFAULT.pixelDataThreadRun threw an exception.
org.quartz.SchedulerException: Job threw an unhandled exception. [See nested exception: org.springframework.scheduling.quartz.JobMethodInvocationFailedException: Invocation of method 'run' on target class [class ome.services.pixeldata.PixelDataThread] failed; nested exception is
ome.conditions.InternalException:  Wrapped Exception: (java.lang.OutOfMemoryError):



How big are these images? How much memory do you have on the server machine? You'll need to increase the -Xmx value under etc/grid/templates.xml in order to handle the images:

Code: Select all


    <server-template id="PixelDataTemplate">
      <parameter name="index"/>
      <parameter name="dir"/>
      <parameter name="config" default="default"/>
      <server id="PixelData-${index}" exe="${JAVA}" activation="always" pwd="${OMERO_HOME}">
        <option>-Xmx256M</option>



Then be sure restart OMERO.

Cheers,
~Josh.

Dear Josh,

thank you for these advices. The image files are typically 2 GB chunks of large datasets. The server has 24 GB memory. I am just a bit confused because the default template.xml had worked fine with the previous version of omero and the same kind of files. Is there some novelty in the way the preview / thumbnail are handled?

In anyway, I modified the template the way you suggested:

jacques@cedre-5a:/var/log/omero$ cat /usr/local/OMERO.server-Current/etc/grid/templates.xml | grep -A10 -B10 -e "<server-template id=\"PixelDataTemplate\">"
<properties>
<properties refid="Basics"/>
<properties refid="JavaServer"/>
<properties refid="Blitz"/>
<properties refid="SingleThreaded"/>
<properties refid="Profile"/>
</properties>
</server>
</server-template>

<server-template id="PixelDataTemplate">
<parameter name="index"/>
<parameter name="dir"/>
<parameter name="config" default="default"/>
<server id="PixelData-${index}" exe="${JAVA}" activation="always" pwd="${OMERO_HOME}">
<option>-Xmx6144M</option>
<option>-Djava.awt.headless=true</option>
<option>-Dlog4j.configuration=${OMERO_ETC}log4j-indexing.xml</option>
<option>-Domero.logfile=${OMERO_LOGFILE}</option>
<option>-Domero.name=PixelData-${index}</option>
<option>-jar</option>

I restarted the server and made a new try with importer, but the symptoms are the same. I attach log file in case of need.

Thank you very much for your help

Jacques

The last part of Blitz.log

Before we just ramp up memory limits again, can we get some sort of information about what these images are? You've said "The image files are typically 2 GB chunks of large datasets." What are the dimensions of these datasets (X-Y dimensions, number of Z-sections, timepoints, channels, etc.)? What is the source data type (TIFF, JPEG, SVS, etc.)?

Hi,

here are the info obtained using fiji import/ virtual stack

Title: 20110629-Spat-1_1.tif
Width: 512 pixels
Height: 512 pixels
Depth: 4086 pixels
Voxel size: 1x1x1 pixel
ID: -4
Coordinate origin: 0,0,0
Bits per pixel: 16 (unsigned)
Display range: 71 - 1979
Image: 1/4086
No Threshold
Uncalibrated
Path: G:\Ahmed\20110529-Spat1-GtubGFP-24hPT\20110629-Spat-1_1.tif
No Selection

=================== And here the metadata seen by LOCI under Fiji ==============
BitsPerPixel 16
DimensionOrder XYCZT
IsInterleaved false
IsRGB false
LittleEndian true
PixelType uint16
SizeC 1
SizeT 4086
SizeX 512
SizeY 512
SizeZ 1
BitsPerSample 16
Compression Uncompressed
ImageLength 512
ImageWidth 512
Location G:\Ahmed\20110529-Spat1-GtubGFP-24hPT\20110629-Spat-1_1.tif
MetaDataPhotometricInterpretation Monochrome
MetaMorph no
NumberOfChannels 1
PhotometricInterpretation BlackIsZero
ResolutionUnit None
XResolution 100
YResolution 100


=================================


I can also upload the image if it helps.
Images are movies done by Andor Solis software usually 15 - 20 min @ 33 fps, cut into chunks of 2 GB by the software itself.

Please let me know if you need further info.

Thank you for your help

Jacques

Having one of the images would be great. Would you also do me a favour and run tiffutil -info or tiffinfo on the TIFF itself?

Code: Select all

$ tiffutil -info G:\Ahmed\20110529-Spat1-GtubGFP-24hPT\20110629-Spat-1_1.tif
$ tiffinfo G:\Ahmed\20110529-Spat1-GtubGFP-24hPT\20110629-Spat-1_1.tif