[ome-devel] Insight problem uploading extremely large datasets
Niko Ehrenfeuchter
nikolaus.ehrenfeuchter at unibas.ch
Mon Jan 12 16:03:47 GMT 2015
Dear all,
one of our users keeps on getting errors when trying to upload
lightsheed datasets into our OMERO. Is this a problem on our side
(configuration / RAM size / ...) or are we just killing Insight with
this massive datasets.
Even though I don't know the exact parameters for this particular one,
it might easily be something in the range of 1-4 TeraBytes.
Thanks for any help
Niko
> omero.ResourceError
> serverStackTrace = "ome.conditions.ResourceError: Cannot mkdir CheckedPath(betcha00_502/2015-01/12):Cannot mkdir CheckedPath(betcha00_502/2015-01/12)
> at ome.services.blitz.repo.RepositoryDaoImpl.internalMkdir(RepositoryDaoImpl.java:887)
> at ome.services.blitz.repo.RepositoryDaoImpl.createOriginalFile(RepositoryDaoImpl.java:860)
> at ome.services.blitz.repo.RepositoryDaoImpl._internalRegister(RepositoryDaoImpl.java:744)
> at ome.services.blitz.repo.RepositoryDaoImpl.register(RepositoryDaoImpl.java:596)
> at ome.services.blitz.repo.PublicRepositoryI.makeCheckedDirs(PublicRepositoryI.java:792)
> at ome.services.blitz.repo.ManagedRepositoryI.makeCheckedDirs(ManagedRepositoryI.java:1343)
> at ome.services.blitz.repo.PublicRepositoryI.makeDir(PublicRepositoryI.java:717)
> at ome.services.blitz.repo.RepositoryDaoImpl$13.doWork(RepositoryDaoImpl.java:706)
> at sun.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:601)
> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
> at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java: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 $Proxy69.doWork(Unknown Source)
> at ome.services.util.Executor$Impl.execute(Executor.java:457)
> at ome.services.blitz.repo.RepositoryDaoImpl.makeDirs(RepositoryDaoImpl.java:693)
> at ome.services.blitz.repo.PublicRepositoryI.makeDir(PublicRepositoryI.java:692)
> at ome.services.blitz.repo.ManagedRepositoryI$TemplateDirectoryCreator.create(ManagedRepositoryI.java:1085)
> at ome.services.blitz.repo.ManagedRepositoryI.expandAndCreateTemplateUserOwnedPath(ManagedRepositoryI.java:1127)
> at ome.services.blitz.repo.ManagedRepositoryI.createTemplatePath(ManagedRepositoryI.java:1152)
> at ome.services.blitz.repo.ManagedRepositoryI.internalImport(ManagedRepositoryI.java:251)
> at ome.services.blitz.repo.ManagedRepositoryI.importFileset(ManagedRepositoryI.java:225)
> at omero.grid._ManagedRepositoryTie.importFileset(_ManagedRepositoryTie.java:66)
> at omero.grid._ManagedRepositoryDisp.___importFileset(_ManagedRepositoryDisp.java:337)
> at omero.grid._ManagedRepositoryDisp.__dispatch(_ManagedRepositoryDisp.java:488)
> at IceInternal.Incoming.invoke(Incoming.java:222)
> at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
> at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
> at Ice.ConnectionI.message(ConnectionI.java:1213)
> at IceInternal.ThreadPool.run(ThreadPool.java:321)
> at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
> at java.lang.Thread.run(Thread.java:722)
> "
> serverExceptionClass = "ome.conditions.ResourceError"
> message = "Cannot mkdir CheckedPath(betcha00_502/2015-01/12):Cannot mkdir CheckedPath(betcha00_502/2015-01/12)"
> 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:357)
> at java.lang.Class.newInstance(Class.java:310)
> at IceInternal.BasicStream.createUserException(BasicStream.java:2615)
> at IceInternal.BasicStream.access$300(BasicStream.java:12)
> at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3099)
> at IceInternal.BasicStream.throwException(BasicStream.java:2077)
> at IceInternal.Outgoing.throwUserException(Outgoing.java:538)
> at omero.grid._ManagedRepositoryDelM.importFileset(_ManagedRepositoryDelM.java:52)
> at omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:83)
> at omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:44)
> at ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:351)
> at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6662)
> at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:233)
> at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1349)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
> at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
> at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
> at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
> at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
> at java.lang.Thread.run(Thread.java:695)
>
> at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6707)
> at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:233)
> at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1349)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
> at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
> at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
> at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
> at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
> at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
> at java.lang.Thread.run(Thread.java:695)
> Caused by: omero.ResourceError
> serverStackTrace = "ome.conditions.ResourceError: Cannot mkdir CheckedPath(betcha00_502/2015-01/12):Cannot mkdir CheckedPath(betcha00_502/2015-01/12)
> at ome.services.blitz.repo.RepositoryDaoImpl.internalMkdir(RepositoryDaoImpl.java:887)
> at ome.services.blitz.repo.RepositoryDaoImpl.createOriginalFile(RepositoryDaoImpl.java:860)
> at ome.services.blitz.repo.RepositoryDaoImpl._internalRegister(RepositoryDaoImpl.java:744)
> at ome.services.blitz.repo.RepositoryDaoImpl.register(RepositoryDaoImpl.java:596)
> at ome.services.blitz.repo.PublicRepositoryI.makeCheckedDirs(PublicRepositoryI.java:792)
> at ome.services.blitz.repo.ManagedRepositoryI.makeCheckedDirs(ManagedRepositoryI.java:1343)
> at ome.services.blitz.repo.PublicRepositoryI.makeDir(PublicRepositoryI.java:717)
> at ome.services.blitz.repo.RepositoryDaoImpl$13.doWork(RepositoryDaoImpl.java:706)
> at sun.reflect.GeneratedMethodAccessor265.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:601)
> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
> at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java: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 $Proxy69.doWork(Unknown Source)
> at ome.services.util.Executor$Impl.execute(Executor.java:457)
> at ome.services.blitz.repo.RepositoryDaoImpl.makeDirs(RepositoryDaoImpl.java:693)
> at ome.services.blitz.repo.PublicRepositoryI.makeDir(PublicRepositoryI.java:692)
> at ome.services.blitz.repo.ManagedRepositoryI$TemplateDirectoryCreator.create(ManagedRepositoryI.java:1085)
> at ome.services.blitz.repo.ManagedRepositoryI.expandAndCreateTemplateUserOwnedPath(ManagedRepositoryI.java:1127)
> at ome.services.blitz.repo.ManagedRepositoryI.createTemplatePath(ManagedRepositoryI.java:1152)
> at ome.services.blitz.repo.ManagedRepositoryI.internalImport(ManagedRepositoryI.java:251)
> at ome.services.blitz.repo.ManagedRepositoryI.importFileset(ManagedRepositoryI.java:225)
> at omero.grid._ManagedRepositoryTie.importFileset(_ManagedRepositoryTie.java:66)
> at omero.grid._ManagedRepositoryDisp.___importFileset(_ManagedRepositoryDisp.java:337)
> at omero.grid._ManagedRepositoryDisp.__dispatch(_ManagedRepositoryDisp.java:488)
> at IceInternal.Incoming.invoke(Incoming.java:222)
> at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
> at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
> at Ice.ConnectionI.message(ConnectionI.java:1213)
> at IceInternal.ThreadPool.run(ThreadPool.java:321)
> at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
> at java.lang.Thread.run(Thread.java:722)
> "
> serverExceptionClass = "ome.conditions.ResourceError"
> message = "Cannot mkdir CheckedPath(betcha00_502/2015-01/12):Cannot mkdir CheckedPath(betcha00_502/2015-01/12)"
> 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:357)
> at java.lang.Class.newInstance(Class.java:310)
> at IceInternal.BasicStream.createUserException(BasicStream.java:2615)
> at IceInternal.BasicStream.access$300(BasicStream.java:12)
> at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3099)
> at IceInternal.BasicStream.throwException(BasicStream.java:2077)
> at IceInternal.Outgoing.throwUserException(Outgoing.java:538)
> at omero.grid._ManagedRepositoryDelM.importFileset(_ManagedRepositoryDelM.java:52)
> at omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:83)
> at omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:44)
> at ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:351)
> at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6662)
> ... 12 more
--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch |
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
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