Hi,<br>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.<br>
Enclosed is the log file that describes my environment. Server runs on Ubuntu 12.04LTS with Java 1.7.0_u11 (all 64-bit).<br>Any suggestions?<br>Thanks,<br>- Damir<br><br>--------------------------<br><br>omero.ResourceError<br>
serverStackTrace = "ome.conditions.ResourceError: Bad file descriptor<br> at ome.services.RawPixelsBean.handleException(RawPixelsBean.java:677)<br> at ome.services.RawPixelsBean.setTile(RawPixelsBean.java:794)<br>
at sun.reflect.GeneratedMethodAccessor990.invoke(Unknown Source)<br> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br> at java.lang.reflect.Method.invoke(Method.java:601)<br>
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)<br>
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)<br> at ome.security.basic.EventHandler.invoke(EventHandler.java:154)<br>
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br> at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)<br>
at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)<br> at $Proxy92.setTile(Unknown Source)<br> at sun.reflect.GeneratedMethodAccessor990.invoke(Unknown Source)<br>
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br> at java.lang.reflect.Method.invoke(Method.java:601)<br> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)<br>
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)<br>
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)<br> at $Proxy92.setTile(Unknown Source)<br> at sun.reflect.GeneratedMethodAccessor992.invoke(Unknown Source)<br>
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br> at java.lang.reflect.Method.invoke(Method.java:601)<br> at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)<br>
at ome.services.throttling.Callback.run(Callback.java:56)<br> at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)<br>
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:150)<br> at ome.services.blitz.impl.RawPixelsStoreI.setTile_async(RawPixelsStoreI.java:268)<br>
at sun.reflect.GeneratedMethodAccessor991.invoke(Unknown Source)<br> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br> at java.lang.reflect.Method.invoke(Method.java:601)<br>
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)<br>
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)<br> at omero.cmd.CallContext.invoke(CallContext.java:59)<br>
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)<br>
at $Proxy93.setTile_async(Unknown Source)<br> at omero.api._RawPixelsStoreTie.setTile_async(_RawPixelsStoreTie.java:318)<br> at omero.api._RawPixelsStoreDisp.___setTile(_RawPixelsStoreDisp.java:1149)<br>
at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1608)<br> at IceInternal.Incoming.invoke(Incoming.java:159)<br> at Ice.ConnectionI.invokeAll(ConnectionI.java:2357)<br>
at Ice.ConnectionI.dispatch(ConnectionI.java:1208)<br> at Ice.ConnectionI.message(ConnectionI.java:1163)<br> at IceInternal.ThreadPool.run(ThreadPool.java:302)<br>
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)<br> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643)<br> at java.lang.Thread.run(Thread.java:722)<br>
"<br> serverExceptionClass = "ome.conditions.ResourceError"<br> message = "Bad file descriptor"<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)<br>
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)<br> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)<br> at java.lang.reflect.Constructor.newInstance(Unknown Source)<br>
at java.lang.Class.newInstance0(Unknown Source)<br> at java.lang.Class.newInstance(Unknown Source)<br> at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)<br> at IceInternal.BasicStream.throwException(BasicStream.java:1632)<br>
at IceInternal.Outgoing.throwUserException(Outgoing.java:442)<br> at omero.api._RawPixelsStoreDelM.setTile(_RawPixelsStoreDelM.java:1774)<br> at omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2435)<br>
at omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2407)<br> at ome.formats.OMEROMetadataStoreClient.setTile(OMEROMetadataStoreClient.java:2502)<br> at ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:889)<br>
at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:801)<br> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:577)<br> at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6443)<br>
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1250)<br> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)<br> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)<br>
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)<br> at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)<br> at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)<br>
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)<br> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)<br> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)<br>
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)<br> at java.lang.Thread.run(Unknown Source)<br><br> at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6492)<br>
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1250)<br> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)<br> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)<br>
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)<br> at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)<br> at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)<br>
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)<br> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)<br> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)<br>
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)<br> at java.lang.Thread.run(Unknown Source)<br>Caused by: omero.ResourceError<br> serverStackTrace = "ome.conditions.ResourceError: Bad file descriptor<br>
at ome.services.RawPixelsBean.handleException(RawPixelsBean.java:677)<br> at ome.services.RawPixelsBean.setTile(RawPixelsBean.java:794)<br> at sun.reflect.GeneratedMethodAccessor990.invoke(Unknown Source)<br>
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br> at java.lang.reflect.Method.invoke(Method.java:601)<br> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)<br>
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)<br>
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)<br> at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)<br> at $Proxy92.setTile(Unknown Source)<br> at sun.reflect.GeneratedMethodAccessor990.invoke(Unknown Source)<br>
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br> at java.lang.reflect.Method.invoke(Method.java:601)<br> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)<br>
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)<br>
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br>
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)<br> at $Proxy92.setTile(Unknown Source)<br> at sun.reflect.GeneratedMethodAccessor992.invoke(Unknown Source)<br>
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br> at java.lang.reflect.Method.invoke(Method.java:601)<br> at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)<br>
at ome.services.throttling.Callback.run(Callback.java:56)<br> at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)<br>
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:150)<br> at ome.services.blitz.impl.RawPixelsStoreI.setTile_async(RawPixelsStoreI.java:268)<br>
at sun.reflect.GeneratedMethodAccessor991.invoke(Unknown Source)<br> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br> at java.lang.reflect.Method.invoke(Method.java:601)<br>
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)<br> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)<br>
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)<br> at omero.cmd.CallContext.invoke(CallContext.java:59)<br>
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)<br> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)<br>
at $Proxy93.setTile_async(Unknown Source)<br> at omero.api._RawPixelsStoreTie.setTile_async(_RawPixelsStoreTie.java:318)<br> at omero.api._RawPixelsStoreDisp.___setTile(_RawPixelsStoreDisp.java:1149)<br>
at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1608)<br> at IceInternal.Incoming.invoke(Incoming.java:159)<br> at Ice.ConnectionI.invokeAll(ConnectionI.java:2357)<br>
at Ice.ConnectionI.dispatch(ConnectionI.java:1208)<br> at Ice.ConnectionI.message(ConnectionI.java:1163)<br> at IceInternal.ThreadPool.run(ThreadPool.java:302)<br>
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)<br> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643)<br> at java.lang.Thread.run(Thread.java:722)<br>
"<br> serverExceptionClass = "ome.conditions.ResourceError"<br> message = "Bad file descriptor"<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)<br>
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)<br> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)<br> at java.lang.reflect.Constructor.newInstance(Unknown Source)<br>
at java.lang.Class.newInstance0(Unknown Source)<br> at java.lang.Class.newInstance(Unknown Source)<br> at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)<br> at IceInternal.BasicStream.throwException(BasicStream.java:1632)<br>
at IceInternal.Outgoing.throwUserException(Outgoing.java:442)<br> at omero.api._RawPixelsStoreDelM.setTile(_RawPixelsStoreDelM.java:1774)<br> at omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2435)<br>
at omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2407)<br> at ome.formats.OMEROMetadataStoreClient.setTile(OMEROMetadataStoreClient.java:2502)<br> at ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:889)<br>
at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:801)<br> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:577)<br> at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6443)<br>
... 11 more<br><br clear="all"><br>-- <br>Damir Sudar - Staff Scientist and Deputy for Technology<br>Lawrence Berkeley Laboratory / Life Sciences Division<br>One Cyclotron Road, MS 977R225A, Berkeley, CA 94720, USA<br>
T: 510/486-5346 - F: 510/486-5586 - E: <a href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a><br>WWW: <a href="http://www.lbl.gov/lifesciences/labs/sudar_lab.html">http://www.lbl.gov/lifesciences/labs/sudar_lab.html</a><br>