[ome-users] Trouble with multiple file export.
Ian Dobbie
ian.dobbie at bioch.ox.ac.uk
Thu Nov 25 09:51:04 GMT 2010
Hi,
I was trying to export multiple files from OMERO.insight client. I
selected the images and then selected the "Export as OME-tiff"
option. This appeared to start fine, working for one file then died. I
then tried to export them separately, which also failed. Restarting
OMERO.insight didn't help. It turned out that the OMERO server process
had run out of file handles. Unfortunately I don't run the server but
our sysadmin came back with this comment.
> Anyway, it really does look like there are too many files open - one
> of the many omero processes (executing java) has over 1000
> filedescriptors open, which I guess could be hitting a limit. Most of
> them (858) are trying to access a delete tiff file named
>
> __omero_export__2729459459188358269.ome.tiff
I just tried again, but this time selecting them separately and doing the
export, but trying to get them to export simultaneously, the same thing
happened. Here is the error log from OMERO.insight.
--------------------------------------------------
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:680)
Caused by: omero.InternalException
serverStackTrace = "java.io.FileNotFoundException: /opt/omeroserv/omero/tmp/omero_omeroserv/3857 at hpslc/__omero_export__3131984980030812120.ome.tiff (Too many open files)
at java.io.RandomAccessFile.open(Native Method)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:100)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:111)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:119)
at loci.common.Location.getHandle(Location.java:196)
at loci.common.Location.getHandle(Location.java:167)
at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:71)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:180)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:211)
at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:247)
at loci.formats.FormatWriter.saveBytes(FormatWriter.java:112)
at loci.formats.ImageWriter.saveBytes(ImageWriter.java:190)
at ome.services.blitz.impl.ExporterI$2.doWork(ExporterI.java:356)
at sun.reflect.GeneratedMethodAccessor209.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$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.FileNotFoundException"
message = "/opt/omeroserv/omero/tmp/omero_omeroserv/3857 at hpslc/__omero_export__3131984980030812120.ome.tiff (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:6352)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6117)
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:4621)
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)
--------------------------------------------------
Thanks,
Ian
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