[ome-devel] Fwd: a problem in our intallation

Lars Kaestner anlkae at uks.eu
Mon Sep 13 10:57:37 BST 2010 

> To whom it may concern,
> Starting from yesterday lunchtime, we have a worsening behavior of our OMERO 4.2 installation. This results in multiple times for successful login up to not being able to open images or Export TIFFs.
> When trying to export OMETIFFs, the following error message pops up.
> We would appreciate any help,
> Peter
> 
> 
> 
> ****************************************************************************
> java.lang.Exception: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data. 
> Cannot export the image as an OME-TIFF
> 	at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:729)
> 	at org.openmicroscopy.shoola.env.data.OMEROGateway.exportImageAsOMETiff(OMEROGateway.java:6405)
> 	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.exportImageAsOMETiff(OmeroImageServiceImpl.java:830)
> 	at org.openmicroscopy.shoola.env.data.views.calls.ExportLoader$1.doCall(ExportLoader.java:76)
> 	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:145)
> 	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
> 	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
> 	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
> 	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
> 	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
> 	at java.lang.Thread.run(Thread.java:637)
> Caused by: omero.InternalException
>    serverStackTrace = "java.io.IOException: Too many open files
>                        	at java.io.UnixFileSystem.createFileExclusively(Native Method)
>                        	at java.io.File.checkAndCreate(File.java:1716)
>                        	at java.io.File.createTempFile(File.java:1804)
>                        	at omero.util.TempFileManager.createPath(TempFileManager.java:320)
>                        	at omero.util.TempFileManager.create_path(TempFileManager.java:429)
>                        	at ome.services.blitz.impl.ExporterI$2.doWork(ExporterI.java:338)
>                        	at sun.reflect.GeneratedMethodAccessor177.invoke(Unknown Source)
>                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>                        	at java.lang.reflect.Method.invoke(Method.java:616)
>                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
>                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
>                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
>                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:409)
>                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:144)
>                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
>                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
>                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:222)
>                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
>                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
>                        	at $Proxy56.doWork(Unknown Source)
>                        	at ome.services.util.Executor$Impl.execute(Executor.java:339)
>                        	at ome.services.blitz.impl.ExporterI.do_tiff(ExporterI.java:315)
>                        	at ome.services.blitz.impl.ExporterI.generateTiff_async(ExporterI.java:185)
>                        	at omero.api._ExporterTie.generateTiff_async(_ExporterTie.java:71)
>                        	at omero.api._ExporterDisp.___generateTiff(_ExporterDisp.java:175)
>                        	at omero.api._ExporterDisp.__dispatch(_ExporterDisp.java:248)
>                        	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 = "java.io.IOException"
>    message = "Too many open files"
> 	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$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
> 	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
> 	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
> 	at omero.api._ExporterDelM.generateTiff(_ExporterDelM.java:79)
> 	at omero.api.ExporterPrxHelper.generateTiff(ExporterPrxHelper.java:117)
> 	at omero.api.ExporterPrxHelper.generateTiff(ExporterPrxHelper.java:89)
> 	at org.openmicroscopy.shoola.env.data.OMEROGateway.exportImageAsOMETiff(OMEROGateway.java:6343)
> 	... 9 more
> 
> 	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:158)
> 	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:245)
> 	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:217)
> 	at org.openmicroscopy.shoola.env.ui.ActivityComponent.showException(ActivityComponent.java:464)
> 	at org.openmicroscopy.shoola.env.ui.ActivityComponent.actionPerformed(ActivityComponent.java:865)
> 	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
> 	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
> 	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
> 	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
> 	at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
> 	at java.awt.Component.processMouseEvent(Component.java:6348)
> 	at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
> 	at java.awt.Component.processEvent(Component.java:6113)
> 	at java.awt.Container.processEvent(Container.java:2085)
> 	at java.awt.Component.dispatchEventImpl(Component.java:4714)
> 	at java.awt.Container.dispatchEventImpl(Container.java:2143)
> 	at java.awt.Component.dispatchEvent(Component.java:4544)
> 	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)
> 	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
> 	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
> 	at java.awt.Container.dispatchEventImpl(Container.java:2129)
> 	at java.awt.Window.dispatchEventImpl(Window.java:2478)
> 	at java.awt.Component.dispatchEvent(Component.java:4544)
> 	at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
> 	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
> 	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
> 	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
> 	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
> 	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
> 	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> 
> ****************************************************************************
> Peter Lipp, PhD
> Head and Professor of Molecular Cell Biology
> Dean of Science
> Institute for Molecular Cell Biology
> Building 61
> Medical Faculty
> Saarland University Hospital
> Saarland University
> 66421 Homburg/Saar
> Germany
> Tel.: +49 6841 162 6103
> Fax.: +49 6841 162 6104
> web: www.lipplab.de

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20100913/ce8976a5/attachment-0001.html>

More information about the ome-devel mailing list