[ome-users] import error

Damir Sudar dsudar at lbl.gov
Fri Jan 18 20:54:36 GMT 2013 

Hi,
Using the Insight Importer I get the error below with one specific large
(3.8GB) LSM file acquired using a Zeiss LSM710. The file has 3 color
channels, 26 Z planes, and is 5120 by 5120 pixels (we used 5 x 5 tiling).
I'll be happy to upload the file somewhere if you have a site that will
accept a ~4GB upload. Note that other (somewhat smaller LSM files acquired
the same way import fine. The offending file is just a bit bigger but ZEN
has no trouble with it.
Enclosed is the log file that describes my environment. Server runs on
Ubuntu 12.04LTS with Java 1.7.0_u11 (all 64-bit).
Any suggestions?
Thanks,
- Damir

--------------------------

omero.ResourceError
    serverStackTrace = "ome.conditions.ResourceError: Bad file descriptor
                            at
ome.services.RawPixelsBean.handleException(RawPixelsBean.java:677)
                            at
ome.services.RawPixelsBean.setTile(RawPixelsBean.java:794)
                            at
sun.reflect.GeneratedMethodAccessor990.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
ome.security.basic.EventHandler.invoke(EventHandler.java:154)
                            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:241)
                            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 $Proxy92.setTile(Unknown Source)
                            at
sun.reflect.GeneratedMethodAccessor990.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
ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98)
                            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 $Proxy92.setTile(Unknown Source)
                            at
sun.reflect.GeneratedMethodAccessor992.invoke(Unknown Source)
                            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                            at
java.lang.reflect.Method.invoke(Method.java:601)
                            at
ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
                            at
ome.services.throttling.Callback.run(Callback.java:56)
                            at
ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
                            at
ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:150)
                            at
ome.services.blitz.impl.RawPixelsStoreI.setTile_async(RawPixelsStoreI.java:268)
                            at
sun.reflect.GeneratedMethodAccessor991.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 $Proxy93.setTile_async(Unknown Source)
                            at
omero.api._RawPixelsStoreTie.setTile_async(_RawPixelsStoreTie.java:318)
                            at
omero.api._RawPixelsStoreDisp.___setTile(_RawPixelsStoreDisp.java:1149)
                            at
omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1608)
                            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)
                        "
    serverExceptionClass = "ome.conditions.ResourceError"
    message = "Bad file descriptor"
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown
Source)
    at java.lang.reflect.Constructor.newInstance(Unknown Source)
    at java.lang.Class.newInstance0(Unknown Source)
    at java.lang.Class.newInstance(Unknown Source)
    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.setTile(_RawPixelsStoreDelM.java:1774)
    at
omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2435)
    at
omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2407)
    at
ome.formats.OMEROMetadataStoreClient.setTile(OMEROMetadataStoreClient.java:2502)
    at
ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:889)
    at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:801)
    at
ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:577)
    at
org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6443)
    at
org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1250)
    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$1.doCall(ImagesImporter.java:110)
    at
org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
    at
org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
    at
org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
    at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
    at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
    at
org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
    at java.lang.Thread.run(Unknown Source)

    at
org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6492)
    at
org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1250)
    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$1.doCall(ImagesImporter.java:110)
    at
org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
    at
org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
    at
org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
    at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
    at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
    at
org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
    at java.lang.Thread.run(Unknown Source)
Caused by: omero.ResourceError
    serverStackTrace = "ome.conditions.ResourceError: Bad file descriptor
                            at
ome.services.RawPixelsBean.handleException(RawPixelsBean.java:677)
                            at
ome.services.RawPixelsBean.setTile(RawPixelsBean.java:794)
                            at
sun.reflect.GeneratedMethodAccessor990.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
ome.security.basic.EventHandler.invoke(EventHandler.java:154)
                            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:241)
                            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 $Proxy92.setTile(Unknown Source)
                            at
sun.reflect.GeneratedMethodAccessor990.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
ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98)
                            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 $Proxy92.setTile(Unknown Source)
                            at
sun.reflect.GeneratedMethodAccessor992.invoke(Unknown Source)
                            at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                            at
java.lang.reflect.Method.invoke(Method.java:601)
                            at
ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
                            at
ome.services.throttling.Callback.run(Callback.java:56)
                            at
ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
                            at
ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:150)
                            at
ome.services.blitz.impl.RawPixelsStoreI.setTile_async(RawPixelsStoreI.java:268)
                            at
sun.reflect.GeneratedMethodAccessor991.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 $Proxy93.setTile_async(Unknown Source)
                            at
omero.api._RawPixelsStoreTie.setTile_async(_RawPixelsStoreTie.java:318)
                            at
omero.api._RawPixelsStoreDisp.___setTile(_RawPixelsStoreDisp.java:1149)
                            at
omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1608)
                            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)
                        "
    serverExceptionClass = "ome.conditions.ResourceError"
    message = "Bad file descriptor"
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown
Source)
    at java.lang.reflect.Constructor.newInstance(Unknown Source)
    at java.lang.Class.newInstance0(Unknown Source)
    at java.lang.Class.newInstance(Unknown Source)
    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.setTile(_RawPixelsStoreDelM.java:1774)
    at
omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2435)
    at
omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2407)
    at
ome.formats.OMEROMetadataStoreClient.setTile(OMEROMetadataStoreClient.java:2502)
    at
ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:889)
    at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:801)
    at
ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:577)
    at
org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6443)
    ... 11 more


-- 
Damir Sudar - Staff Scientist and Deputy for Technology
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977R225A, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
WWW: http://www.lbl.gov/lifesciences/labs/sudar_lab.html
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