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Task #13087 (new)

Opened 4 years ago

Last modified 4 years ago

BUG: Freezes at import of archived

Reported by: pwalczysko Owned by: jburel
Priority: major Milestone: FacilityManagers
Component: Insight Version: OMERO-5.2.0-m0
Keywords: n.a. Cc: ux@…, mporter
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Originally reported by mporter

  • find any archived images (see http://trac.openmicroscopy.org/ome/ticket/13086#comment:1 for where they are)
  • start importing any of them (Windows or Mac, repeatable on both)
  • observe that after you added even a single such image into the queue, then after the "Scanning" phase starts and you click onto the "Select Data to Import" tab or into the main Insight window, then
  • there is no reaction, the insight freezes, the progress spinners stop spinning in importer
  • this is intermittent, and does not have any influence on success or failure of the import
  • from the Insight log:
2015-10-30 12:43:54,062 INFO  [      o.f.i.transfers.UploadFileTransfer] ( Thread-62) Transferring /Volumes/lmf/mporter/150917_Jasp-spindles/RPE1_CAG_1000nM_Jasp_MT_01_05_R3D_D3D_log.txt... 
2015-10-30 12:43:54,695 DEBUG [                 omero.gateway.Connector] ( Thread-62) Close import store OMEROMetadataStoreClient nImportStore=2 
2015-10-30 12:43:54,749 WARN  [    ome.formats.OMEROMetadataStoreClient] ( Thread-62) Exception closing 27edb9c2-2acb-4649-8b85-99f1842de92f/e0ba5b0f-ce82-42d3-9cb7-6ea82f7807d4omero.api.MetadataStore -t -e 1.0:tcp -h eel.openmicroscopy.org -p 46661 
Ice.ObjectNotExistException: null
	at IceInternal.Outgoing.invoke(Outgoing.java:158) ~[ice.jar:na]
	at omero.api._MetadataStoreDelM.close(_MetadataStoreDelM.java:412) ~[blitz.jar:na]
	at omero.api.MetadataStorePrxHelper.close(MetadataStorePrxHelper.java:1560) ~[blitz.jar:na]
	at omero.api.MetadataStorePrxHelper.close(MetadataStorePrxHelper.java:1522) ~[blitz.jar:na]
	at ome.formats.OMEROMetadataStoreClient.closeQuietly(OMEROMetadataStoreClient.java:1053) [blitz.jar:na]
	at ome.formats.OMEROMetadataStoreClient.closeServices(OMEROMetadataStoreClient.java:1083) [blitz.jar:na]
	at omero.gateway.Connector.shutdownImports(Connector.java:750) [blitz.jar:na]
	at omero.gateway.Connector.closeImport(Connector.java:617) [blitz.jar:na]
	at omero.gateway.Gateway.closeImport(Gateway.java:362) [blitz.jar:na]
	at org.openmicroscopy.shoola.env.data.OMEROGateway.closeImport(OMEROGateway.java:7174) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:5962) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1204) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) [omero.insight.jar:na]
	at java.lang.Thread.run(Thread.java:745) [na:1.8.0_65]
2015-10-30 12:43:54,750 DEBUG [                 omero.gateway.Connector] ( Thread-62) Close import store OMEROMetadataStoreClient nImportStore=1 
2015-10-30 12:43:54,796 WARN  [    ome.formats.OMEROMetadataStoreClient] ( Thread-62) Exception closing 27edb9c2-2acb-4649-8b85-99f1842de92f/e0ba5b0f-ce82-42d3-9cb7-6ea82f7807d4omero.api.MetadataStore -t -e 1.0:tcp -h eel.openmicroscopy.org -p 46661 
Ice.ObjectNotExistException: null
	at IceInternal.Outgoing.invoke(Outgoing.java:158) ~[ice.jar:na]
	at omero.api._MetadataStoreDelM.close(_MetadataStoreDelM.java:412) ~[blitz.jar:na]
	at omero.api.MetadataStorePrxHelper.close(MetadataStorePrxHelper.java:1560) ~[blitz.jar:na]
	at omero.api.MetadataStorePrxHelper.close(MetadataStorePrxHelper.java:1522) ~[blitz.jar:na]
	at ome.formats.OMEROMetadataStoreClient.closeQuietly(OMEROMetadataStoreClient.java:1053) [blitz.jar:na]
	at ome.formats.OMEROMetadataStoreClient.closeServices(OMEROMetadataStoreClient.java:1083) [blitz.jar:na]
	at omero.gateway.Connector.shutdownImports(Connector.java:750) [blitz.jar:na]
	at omero.gateway.Connector.closeImport(Connector.java:617) [blitz.jar:na]
	at omero.gateway.Gateway.closeImport(Gateway.java:362) [blitz.jar:na]
	at org.openmicroscopy.shoola.env.data.OMEROGateway.closeImport(OMEROGateway.java:7174) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:5962) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1204) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) [omero.insight.jar:na]
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) [omero.insight.jar:na]
	at java.lang.Thread.run(Thread.java:745) [na:1.8.0_65]
2015-10-30 12:43:54,796 DEBUG [                 omero.gateway.Connector] ( Thread-62) Close import store OMEROMetadataStoreClient nImportStore=0 
2015-10-30 12:43:57,292 DEBUG [                 omero.gateway.Connector] (entQueue-0) Create stateful service omero.api.ThumbnailStore nStateful=1 
2015-10-30 12:43:57,343 DEBUG [                 omero.gateway.Connector] ( Thread-69) Close stateful service ThumbnailStorePrxHelper nStateful=0 

Change History (5)

comment:1 Changed 4 years ago by pwalczysko

the jstack of the process as the insight was frozen

jstack 85888
2015-10-30 14:36:06
Full thread dump Java HotSpot(TM) 64-Bit Server VM (25.65-b01 mixed mode):

"Attach Listener" #105 daemon prio=9 os_prio=31 tid=0x00007fcc0a8f4800 nid=0x1437f waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Thread-25" #104 prio=6 os_prio=31 tid=0x00007fcc15382800 nid=0x1026b runnable [0x0000000195ede000]
   java.lang.Thread.State: RUNNABLE
	at sun.nio.ch.FileDispatcherImpl.pread0(Native Method)
	at sun.nio.ch.FileDispatcherImpl.pread(FileDispatcherImpl.java:52)
	at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:220)
	at sun.nio.ch.IOUtil.read(IOUtil.java:197)
	at sun.nio.ch.FileChannelImpl.readInternal(FileChannelImpl.java:740)
	at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:726)
	at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:127)
	at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:112)
	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:600)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:126)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:139)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:148)
	at loci.common.Location.getHandle(Location.java:324)
	at loci.common.Location.getHandle(Location.java:294)
	at loci.common.Location.getHandle(Location.java:284)
	at loci.common.Location.getHandle(Location.java:274)
	at loci.common.Location.checkValidId(Location.java:349)
	at loci.formats.ImageReader.getReader(ImageReader.java:173)
	at loci.formats.ImageReader.setId(ImageReader.java:832)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.Memoizer.setId(Memoizer.java:650)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:410)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:566)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:367)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5989)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1035)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:745)

"Ice.ThreadPool.Client-9" #100 prio=5 os_prio=31 tid=0x00007fcc0a8f8000 nid=0xac4f in Object.wait() [0x0000000192e61000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at IceInternal.ThreadPool.followerWait(ThreadPool.java:573)
	- locked <0x0000000780749950> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.run(ThreadPool.java:363)
	- locked <0x0000000780749950> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.ThreadPool.Client-9" #99 prio=5 os_prio=31 tid=0x00007fcc15ae4000 nid=0xaa2b in Object.wait() [0x0000000191a37000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at IceInternal.ThreadPool.followerWait(ThreadPool.java:573)
	- locked <0x00000007807d06d0> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.run(ThreadPool.java:363)
	- locked <0x00000007807d06d0> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.ThreadPool.Client-9" #98 prio=5 os_prio=31 tid=0x00007fcc15ae3000 nid=0x12223 in Object.wait() [0x0000000191620000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at IceInternal.ThreadPool.followerWait(ThreadPool.java:573)
	- locked <0x000000078092b9a8> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.run(ThreadPool.java:363)
	- locked <0x000000078092b9a8> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.ThreadPool.Client-8" #90 prio=5 os_prio=31 tid=0x00007fcc09b48800 nid=0x12c1f in Object.wait() [0x000000018ee70000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at IceInternal.ThreadPool.followerWait(ThreadPool.java:573)
	- locked <0x0000000780749950> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.run(ThreadPool.java:394)
	- locked <0x0000000780749950> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.ThreadPool.Client-8" #89 prio=5 os_prio=31 tid=0x00007fcc15878800 nid=0x12d1f in Object.wait() [0x0000000121d79000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at IceInternal.ThreadPool.followerWait(ThreadPool.java:573)
	- locked <0x0000000780951150> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.run(ThreadPool.java:363)
	- locked <0x0000000780951150> (a IceInternal.ThreadPool)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.ThreadPool.Client-0" #46 prio=5 os_prio=31 tid=0x00007fcc0c40e800 nid=0x13203 runnable [0x0000000192d5e000]
   java.lang.Thread.State: RUNNABLE
	at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
	at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:198)
	at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:103)
	at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
	- locked <0x00000007807d0970> (a sun.nio.ch.Util$2)
	- locked <0x00000007807d0980> (a java.util.Collections$UnmodifiableSet)
	- locked <0x00000007807d0920> (a sun.nio.ch.KQueueSelectorImpl)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
	at IceInternal.Selector.select(Selector.java:263)
	at IceInternal.ThreadPool.run(ThreadPool.java:338)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.HostResolver" #45 prio=5 os_prio=31 tid=0x00007fcc0a021000 nid=0x13003 in Object.wait() [0x0000000192c5b000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:167)
	- locked <0x00000007807d0b80> (a IceInternal.EndpointHostResolver)
	at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:290)

"Ice.Timer" #44 prio=5 os_prio=31 tid=0x00007fcc0a020800 nid=0x12e03 in Object.wait() [0x0000000192b58000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.Timer.run(Timer.java:185)
	- locked <0x00000007807d0ba8> (a IceInternal.Timer)

"Ice.ThreadPool.Client-0" #42 prio=5 os_prio=31 tid=0x00007fcc0a3e9000 nid=0x12a03 runnable [0x0000000192952000]
   java.lang.Thread.State: RUNNABLE
	at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
	at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:198)
	at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:103)
	at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
	- locked <0x0000000780988d50> (a sun.nio.ch.Util$2)
	- locked <0x0000000780989030> (a java.util.Collections$UnmodifiableSet)
	- locked <0x0000000780988ac8> (a sun.nio.ch.KQueueSelectorImpl)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
	at IceInternal.Selector.select(Selector.java:263)
	at IceInternal.ThreadPool.run(ThreadPool.java:338)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.HostResolver" #41 prio=5 os_prio=31 tid=0x00007fcc0abcd000 nid=0x12803 in Object.wait() [0x000000019284f000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:167)
	- locked <0x00000007809a2810> (a IceInternal.EndpointHostResolver)
	at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:290)

"Ice.Timer" #40 prio=5 os_prio=31 tid=0x00007fcc0a88e800 nid=0x12603 in Object.wait() [0x000000019274c000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.Timer.run(Timer.java:185)
	- locked <0x000000078098f838> (a IceInternal.Timer)

"Ice.ThreadPool.Client-1" #39 prio=5 os_prio=31 tid=0x00007fcc0b06d800 nid=0x12403 runnable [0x0000000192649000]
   java.lang.Thread.State: RUNNABLE
	at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
	at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:198)
	at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:103)
	at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
	- locked <0x0000000780749a38> (a sun.nio.ch.Util$2)
	- locked <0x000000078077c728> (a java.util.Collections$UnmodifiableSet)
	- locked <0x00000007807496d0> (a sun.nio.ch.KQueueSelectorImpl)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
	at IceInternal.Selector.select(Selector.java:263)
	at IceInternal.ThreadPool.run(ThreadPool.java:338)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.HostResolver" #37 prio=5 os_prio=31 tid=0x00007fcc09b11000 nid=0x12007 in Object.wait() [0x0000000192443000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:167)
	- locked <0x00000007807ca148> (a IceInternal.EndpointHostResolver)
	at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:290)

"Ice.Timer" #36 prio=5 os_prio=31 tid=0x00007fcc09810000 nid=0x11e2f in Object.wait() [0x0000000192340000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.Timer.run(Timer.java:185)
	- locked <0x000000078077cce0> (a IceInternal.Timer)

"pool-1-thread-1" #34 prio=5 os_prio=31 tid=0x00007fcc0a9c5000 nid=0x9f0f waiting on condition [0x000000019203d000]
   java.lang.Thread.State: TIMED_WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00000007809e4818> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
	at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)
	at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

"Ice.ThreadPool.Client-1" #33 prio=5 os_prio=31 tid=0x00007fcc0b079800 nid=0xa60b runnable [0x0000000191f3a000]
   java.lang.Thread.State: RUNNABLE
	at sun.nio.ch.KQueueArrayWrapper.kevent0(Native Method)
	at sun.nio.ch.KQueueArrayWrapper.poll(KQueueArrayWrapper.java:198)
	at sun.nio.ch.KQueueSelectorImpl.doSelect(KQueueSelectorImpl.java:103)
	at sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
	- locked <0x00000007809511e0> (a sun.nio.ch.Util$2)
	- locked <0x0000000780951c58> (a java.util.Collections$UnmodifiableSet)
	- locked <0x0000000780950ed0> (a sun.nio.ch.KQueueSelectorImpl)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
	at sun.nio.ch.SelectorImpl.select(SelectorImpl.java:101)
	at IceInternal.Selector.select(Selector.java:263)
	at IceInternal.ThreadPool.run(ThreadPool.java:338)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:745)

"Ice.HostResolver" #31 prio=5 os_prio=31 tid=0x00007fcc09800000 nid=0x721f in Object.wait() [0x0000000191934000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.EndpointHostResolver.run(EndpointHostResolver.java:167)
	- locked <0x0000000780993828> (a IceInternal.EndpointHostResolver)
	at IceInternal.EndpointHostResolver$HelperThread.run(EndpointHostResolver.java:290)

"Ice.Timer" #30 prio=5 os_prio=31 tid=0x00007fcc09d53800 nid=0x230b in Object.wait() [0x000000019131b000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at IceInternal.Timer.run(Timer.java:185)
	- locked <0x0000000780954ab0> (a IceInternal.Timer)

"net.sf.ehcache.CacheManager@15747442" #22 daemon prio=5 os_prio=31 tid=0x00007fcc0c38b800 nid=0x11607 in Object.wait() [0x000000018ecca000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.util.TimerThread.mainLoop(Timer.java:552)
	- locked <0x0000000780059708> (a java.util.TaskQueue)
	at java.util.TimerThread.run(Timer.java:505)

"TimerQueue" #21 daemon prio=5 os_prio=31 tid=0x00007fcc0a3e2000 nid=0x10d53 waiting on condition [0x0000000190131000]
   java.lang.Thread.State: TIMED_WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00000007800598e0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
	at java.util.concurrent.DelayQueue.take(DelayQueue.java:223)
	at javax.swing.TimerQueue.run(TimerQueue.java:171)
	at java.lang.Thread.run(Thread.java:745)

"AWT-EventQueue-0" #19 prio=6 os_prio=31 tid=0x00007fcc0a2a1800 nid=0xf00b runnable [0x000000018f12f000]
   java.lang.Thread.State: RUNNABLE
	at java.io.UnixFileSystem.getBooleanAttributes0(Native Method)
	at java.io.UnixFileSystem.getBooleanAttributes(UnixFileSystem.java:242)
	at java.io.File.isDirectory(File.java:849)
	at sun.awt.shell.ShellFolder.isDirectory(ShellFolder.java:378)
	at loci.formats.gui.ExtensionFileFilter.accept(ExtensionFileFilter.java:97)
	at loci.formats.gui.ComboFileFilter.accept(ComboFileFilter.java:128)
	at javax.swing.JFileChooser.accept(JFileChooser.java:1650)
	at com.apple.laf.AquaFileChooserUI$FCSubpanel.isSelectableInList(AquaFileChooserUI.java:1904)
	at com.apple.laf.AquaFileChooserUI.isSelectableInList(AquaFileChooserUI.java:545)
	at com.apple.laf.AquaFileChooserUI$FileRenderer.getTableCellRendererComponent(AquaFileChooserUI.java:1105)
	at javax.swing.JTable.prepareRenderer(JTable.java:5723)
	at javax.swing.plaf.basic.BasicTableUI.paintCell(BasicTableUI.java:2114)
	at javax.swing.plaf.basic.BasicTableUI.paintCells(BasicTableUI.java:2016)
	at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1812)
	at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
	at javax.swing.JComponent.paintComponent(JComponent.java:780)
	at javax.swing.JComponent.paint(JComponent.java:1056)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JViewport.paint(JViewport.java:728)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1047)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintChildren(JComponent.java:889)
	- locked <0x00000007800013d0> (a java.awt.Component$AWTTreeLock)
	at javax.swing.JComponent.paint(JComponent.java:1065)
	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
	at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
	at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
	at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
	at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
	at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
	at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
	at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
	at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

"AWT-Shutdown" #20 prio=5 os_prio=31 tid=0x00007fcc0a32c000 nid=0x8513 in Object.wait() [0x000000018f02f000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:295)
	- locked <0x0000000780059cc8> (a java.lang.Object)
	at java.lang.Thread.run(Thread.java:745)

"Timer-0" #17 daemon prio=5 os_prio=31 tid=0x00007fcc09b7a000 nid=0xeb03 in Object.wait() [0x00000001223f5000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.util.TimerThread.mainLoop(Timer.java:552)
	- locked <0x0000000780039900> (a java.util.TaskQueue)
	at java.util.TimerThread.run(Timer.java:505)

"Java2D Disposer" #16 daemon prio=10 os_prio=31 tid=0x00007fcc09b79800 nid=0xe80b in Object.wait() [0x00000001220a3000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
	- locked <0x0000000780059e78> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
	at sun.java2d.Disposer.run(Disposer.java:148)
	at java.lang.Thread.run(Thread.java:745)

"Java2D Queue Flusher" #15 daemon prio=10 os_prio=31 tid=0x00007fcc09a60800 nid=0xdc0b in Object.wait() [0x0000000121ec0000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run(OGLRenderQueue.java:203)
	- locked <0x0000000780056e68> (a sun.java2d.opengl.OGLRenderQueue$QueueFlusher)

"AppKit Thread" #12 daemon prio=5 os_prio=31 tid=0x00007fcc0a007000 nid=0x130f runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"DestroyJavaVM" #11 prio=5 os_prio=31 tid=0x00007fcc0c02c800 nid=0x330b waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Service Thread" #9 daemon prio=9 os_prio=31 tid=0x00007fcc0a8dc000 nid=0x5e03 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C1 CompilerThread3" #8 daemon prio=9 os_prio=31 tid=0x00007fcc0a01a000 nid=0x5c03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread2" #7 daemon prio=9 os_prio=31 tid=0x00007fcc0a019800 nid=0x5a03 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread1" #6 daemon prio=9 os_prio=31 tid=0x00007fcc0a015800 nid=0x5803 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" #5 daemon prio=9 os_prio=31 tid=0x00007fcc0a83f000 nid=0x5603 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" #4 daemon prio=9 os_prio=31 tid=0x00007fcc0a015000 nid=0x530f runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" #3 daemon prio=8 os_prio=31 tid=0x00007fcc0a864800 nid=0x5003 in Object.wait() [0x000000011cacf000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
	- locked <0x0000000780057b78> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)

"Reference Handler" #2 daemon prio=10 os_prio=31 tid=0x00007fcc0a864000 nid=0x4e03 in Object.wait() [0x000000011c9cc000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)
	- locked <0x0000000780057f20> (a java.lang.ref.Reference$Lock)

"VM Thread" os_prio=31 tid=0x00007fcc0a80e800 nid=0x4c03 runnable 

"GC task thread#0 (ParallelGC)" os_prio=31 tid=0x00007fcc0a011000 nid=0x3c03 runnable 

"GC task thread#1 (ParallelGC)" os_prio=31 tid=0x00007fcc09813800 nid=0x3e03 runnable 

"GC task thread#2 (ParallelGC)" os_prio=31 tid=0x00007fcc0a011800 nid=0x4003 runnable 

"GC task thread#3 (ParallelGC)" os_prio=31 tid=0x00007fcc0a012000 nid=0x4203 runnable 

"GC task thread#4 (ParallelGC)" os_prio=31 tid=0x00007fcc0a804800 nid=0x4403 runnable 

"GC task thread#5 (ParallelGC)" os_prio=31 tid=0x00007fcc0a805000 nid=0x4603 runnable 

"GC task thread#6 (ParallelGC)" os_prio=31 tid=0x00007fcc0a808800 nid=0x4803 runnable 

"GC task thread#7 (ParallelGC)" os_prio=31 tid=0x00007fcc0a809800 nid=0x4a03 runnable 

"VM Periodic Task Thread" os_prio=31 tid=0x00007fcc0a838800 nid=0x6003 waiting on condition 

JNI global references: 8323

comment:2 Changed 4 years ago by pwalczysko

I can repeat this on 5.1.4 release insight client connected to trout -> not a regression

comment:3 Changed 4 years ago by jburel

  • Milestone changed from OMERO-5.2.1 to OMERO-5.2.2

Milestone OMERO-5.2.1 deleted

comment:4 Changed 4 years ago by jburel

  • Milestone changed from OMERO-5.2.2 to OMERO-5.2.1

Milestone OMERO-5.2.2 deleted

comment:5 Changed 4 years ago by jburel

  • Milestone changed from OMERO-5.2.2 to FacilityManagers
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