[ome-devel] OMERO upload problems
Niko Ehrenfeuchter
nikolaus.ehrenfeuchter at unibas.ch
Thu Feb 27 15:59:54 GMT 2014
Hi all,
one of our users reported problems with uploading to OMERO with the
error message below. He is one of our power users already having
uploaded giant datasets into OMERO. According to him this problem occurs
more or less randomly, however he notes this dataset has an unusual high
amount of timepoints - maybe that's related?
The MemoryLimitException below complains about a ridicoulous amount of
RAM (64MB) being requested by this particular step, so maybe we have a
bug somewhere in our configuration?
Thanks a lot in advance
Niko
> Ice.UnknownLocalException
> unknown = "Ice::MemoryLimitException
> Ice.MemoryLimitException
> reason = "requested 67108872 bytes, maximum allowed is 67108864 bytes (see Ice.MessageSizeMax)"
> at IceInternal.Ex.throwMemoryLimitException(Ex.java:23)
> at IceInternal.BasicStream.expand(BasicStream.java:2049)
> at IceInternal.BasicStream.writeLong(BasicStream.java:964)
> at omero.sys.LongListHelper.write(LongListHelper.java:37)
> at omero.sys.EventContext.__write(EventContext.java:136)
> at IceInternal.BasicStream.writeInstance(BasicStream.java:1721)
> at IceInternal.BasicStream.writePendingObjects(BasicStream.java:1639)
> at omero.api._AMD_MetadataStore_saveToDB.ice_response(_AMD_MetadataStore_saveToDB.java:40)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:601)
> at ome.services.throttling.Task.response(Task.java:63)
> at ome.services.throttling.Adapter.run(Adapter.java:63)
> at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
> at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:163)
> at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:190)
> at sun.reflect.GeneratedMethodAccessor1360.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:601)
> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
> at omero.cmd.CallContext.invoke(CallContext.java:59)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
> at $Proxy107.saveToDB_async(Unknown Source)
> at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:94)
> at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:266)
> at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:414)
> at IceInternal.Incoming.invoke(Incoming.java:159)
> at Ice.ConnectionI.invokeAll(ConnectionI.java:2357)
> at Ice.ConnectionI.dispatch(ConnectionI.java:1208)
> at Ice.ConnectionI.message(ConnectionI.java:1163)
> at IceInternal.ThreadPool.run(ThreadPool.java:302)
> at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643)
> at java.lang.Thread.run(Thread.java:722)
> "
> at IceInternal.Outgoing.invoke(Outgoing.java:158)
> at omero.api._MetadataStoreDelM.saveToDB(_MetadataStoreDelM.java:167)
> at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:573)
> at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:545)
> at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2122)
> at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:368)
> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:550)
> at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6400)
> at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1350)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
> at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
> at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
> at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
> at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
> at java.lang.Thread.run(Thread.java:695)
>
> at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6454)
> at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1350)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
> at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
> at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
> at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
> at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
> at java.lang.Thread.run(Thread.java:695)
> Caused by: Ice.UnknownLocalException
> unknown = "Ice::MemoryLimitException
> Ice.MemoryLimitException
> reason = "requested 67108872 bytes, maximum allowed is 67108864 bytes (see Ice.MessageSizeMax)"
> at IceInternal.Ex.throwMemoryLimitException(Ex.java:23)
> at IceInternal.BasicStream.expand(BasicStream.java:2049)
> at IceInternal.BasicStream.writeLong(BasicStream.java:964)
> at omero.sys.LongListHelper.write(LongListHelper.java:37)
> at omero.sys.EventContext.__write(EventContext.java:136)
> at IceInternal.BasicStream.writeInstance(BasicStream.java:1721)
> at IceInternal.BasicStream.writePendingObjects(BasicStream.java:1639)
> at omero.api._AMD_MetadataStore_saveToDB.ice_response(_AMD_MetadataStore_saveToDB.java:40)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:601)
> at ome.services.throttling.Task.response(Task.java:63)
> at ome.services.throttling.Adapter.run(Adapter.java:63)
> at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
> at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:163)
> at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:190)
> at sun.reflect.GeneratedMethodAccessor1360.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:601)
> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
> at omero.cmd.CallContext.invoke(CallContext.java:59)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
> at $Proxy107.saveToDB_async(Unknown Source)
> at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:94)
> at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:266)
> at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:414)
> at IceInternal.Incoming.invoke(Incoming.java:159)
> at Ice.ConnectionI.invokeAll(ConnectionI.java:2357)
> at Ice.ConnectionI.dispatch(ConnectionI.java:1208)
> at Ice.ConnectionI.message(ConnectionI.java:1163)
> at IceInternal.ThreadPool.run(ThreadPool.java:302)
> at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643)
> at java.lang.Thread.run(Thread.java:722)
> "
> at IceInternal.Outgoing.invoke(Outgoing.java:158)
> at omero.api._MetadataStoreDelM.saveToDB(_MetadataStoreDelM.java:167)
> at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:573)
> at omero.api.MetadataStorePrxHelper.saveToDB(MetadataStorePrxHelper.java:545)
> at ome.formats.OMEROMetadataStoreClient.saveToDB(OMEROMetadataStoreClient.java:2122)
> at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:368)
> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:550)
> at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6400)
> ... 11 more
--
Niko Ehrenfeuchter
Imaging Core Facility
Kragenbau, Room G1055
Biozentrum, University of Basel
Klingelbergstrasse 50/70
CH-4056 Basel (Switzerland)
Office: +41 (61) 26 72673
Email: nikolaus.ehrenfeuchter at unibas.ch
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