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Task #6083 (closed)

Opened 8 years ago

Closed 8 years ago

Bug: lsm file > 4GB failed to import

Reported by: cblackburn Owned by: cxallan
Priority: major Milestone: OMERO-Beta4.3.1
Component: Import Version: n.a.
Keywords: n.a. Cc: cxallan, mlinkert
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-07-07 (1)

Description (last modified by cxallan)

Attempting to import the file:

All_tub_40_25min_15Sum.lsm

using server on Ubuntu 9.10 and client on MacOS X. (Too large for remote import to howe!) A smaller 128MB lsm file was okay on the same server/client combination.

Attachments (2)

Blitz-0.log.zip​ (896.8 KB) - added by cblackburn 8 years ago.
zct_md.patch​ (1.2 KB) - added by cxallan 8 years ago.
Patch using ZCT and planar message digest updates

Download all attachments as: .zip

Change History (6)

comment:1 Changed 8 years ago by cxallan

  • Description modified (diff)

Stack trace:

omero.ResourceError
    serverStackTrace = "ome.conditions.ResourceError: Map failed
                        	at ome.services.RawPixelsBean.save(RawPixelsBean.java:194)
                        	at ome.services.RawPixelsBean.close(RawPixelsBean.java:208)
                        	at sun.reflect.GeneratedMethodAccessor700.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                        	at java.lang.reflect.Method.invoke(Method.java:616)
                        	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 ome.security.basic.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy80.close(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor700.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                        	at java.lang.reflect.Method.invoke(Method.java:616)
                        	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 ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
                        	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 $Proxy80.close(Unknown Source)
                        	at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:227)
                        	at omero.api._RawPixelsStoreTie.close_async(_RawPixelsStoreTie.java:330)
                        	at omero.api._StatefulServiceInterfaceDisp.___close(_StatefulServiceInterfaceDisp.java:142)
                        	at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1157)
                        	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 = "ome.conditions.ResourceError"
    message = "Map failed"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._RawPixelsStoreDelM.close(_RawPixelsStoreDelM.java:1901)
	at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2642)
	at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2614)
	at ome.formats.OMEROMetadataStoreClient.finalizePixelStore(OMEROMetadataStoreClient.java:2458)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:508)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6314)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1175)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6359)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1175)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: omero.ResourceError
    serverStackTrace = "ome.conditions.ResourceError: Map failed
                        	at ome.services.RawPixelsBean.save(RawPixelsBean.java:194)
                        	at ome.services.RawPixelsBean.close(RawPixelsBean.java:208)
                        	at sun.reflect.GeneratedMethodAccessor700.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                        	at java.lang.reflect.Method.invoke(Method.java:616)
                        	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 ome.security.basic.EventHandler.invoke(EventHandler.java:150)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy80.close(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor700.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                        	at java.lang.reflect.Method.invoke(Method.java:616)
                        	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 ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
                        	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 $Proxy80.close(Unknown Source)
                        	at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:227)
                        	at omero.api._RawPixelsStoreTie.close_async(_RawPixelsStoreTie.java:330)
                        	at omero.api._StatefulServiceInterfaceDisp.___close(_StatefulServiceInterfaceDisp.java:142)
                        	at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1157)
                        	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 = "ome.conditions.ResourceError"
    message = "Map failed"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._RawPixelsStoreDelM.close(_RawPixelsStoreDelM.java:1901)
	at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2642)
	at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2614)
	at ome.formats.OMEROMetadataStoreClient.finalizePixelStore(OMEROMetadataStoreClient.java:2458)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:508)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6314)
	... 11 more

comment:2 Changed 8 years ago by cxallan

  • Owner set to cxallan
  • Remaining Time set to 0.25

comment:3 Changed 8 years ago by cxallan

  • Status changed from new to accepted

Changed 8 years ago by cblackburn

Changed 8 years ago by cxallan

Patch using ZCT and planar message digest updates

comment:4 Changed 8 years ago by cxallan

  • Remaining Time changed from 0.25 to 0
  • Resolution set to worksforme
  • Status changed from accepted to closed

Verified to import successfully on a server running on a 64-bit platform. Known limitation added to the OMERO.server troubleshooting page:

http://www.openmicroscopy.org/site/support/omero4/troubleshooting

Closing as worksforme.

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