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

Josh Moore josh.moore at gmx.de
Mon Sep 13 12:00:46 BST 2010


Hi Lars,

for any site doing a significant number of exports this is a known issue:

 http://trac.openmicroscopy.org.uk/omero/ticket/2764

which will be fixed in the upcoming 4.2.1 release. Restarting the server will reset the number of open files, but the same problem will re-occur after some number of exports.

Until the patch release, possible workarounds are:


* Periodically restart the server.
* Increase the number of open files for the Blitz process
* Install a newer bioformats version (EXPERIMENTAL)


To find out how many export files your process has hanging around, find out the PID and then:

/tmp/omero_dist $ lsof -p 67602 | grep export
java    67602 moore  123u     REG       14,2     33213 14257076 .../__omero_export__1572328266581768206.ome.tiff
/tmp/omero_dist $ lsof -p 67602 | grep export | wc -l
      1

Here, one means that I have one export file hanging around. As that approaches the number of allowed open-files, the OMERO server will start to misbehave.

To find out how many open files are permitted, use:

/tmp/omero_dist $ ulimit -n
256

To change the value, stop your server, change the value and restart:
/tmp/omero_dist $ bin/omero admin stop
Waiting on shutdown. Use CTRL-C to exit
/tmp/omero_dist $ ulimit -n 8096
/tmp/omero_dist $ ulimit -n
8096

(or permantently in /etc/sysctl.conf on Mac and /etc/security on Linux)


/tmp/omero_dist $ bin/omero admin start
...

If someone on your side is interested in testing the Bio-Formats solution, we may be able to backport the fix. Please let us know, and we can being talk through the steps.

Best wishes,
~Josh.


On Sep 13, 2010, at 11:57 AM, Lars Kaestner wrote:

> 
>> 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)
>> 
>> 



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