dhis2-devs team mailing list archive

[Jason Pickering <jason.p.pickering@xxxxxxxxx>]

Seems like a memory issue

 java.lang.OutOfMemoryError: GC overhead limit exceeded

On Fri, Oct 14, 2016, 13:35 Jose Garcia Muñoz <josemp10@xxxxxxxxx> wrote:

>
> Thanks Lars,
>
> I have run data integrity, but the system has passed "Organisation units
> with cyclic references ". I didn't get any errors importing events, but
> aggregated... Will try to divide the file in small chunks to try to figure
> it out...
>
> Thanks
> Jose
>
> On Fri, Oct 14, 2016 at 11:02 AM, Lars Helge Øverland <lars@xxxxxxxxx>
> wrote:
>
> Hi Jose,
>
> my best guess here is a cyclic parent relationship in the org unit
> hierarchy, i.e. you have one or more org units where the one of the
> ancestors are also a child.
>
> Try running data admin > integrity checks and look for "Organisation units
> with cyclic references ", or look for it through SQL.
>
> best regards,
>
> Lars
>
>
> On Fri, Oct 14, 2016 at 1:09 AM, Jose Garcia Muñoz <josemp10@xxxxxxxxx>
> wrote:
>
>
> Dear devs,
>
> I'm trying to import an XML file (900K) with around 8.000 datavalues in
> 2.24 (build revision 1502fe2). However, I'm getting 2 different kind of
> errors during the import... (attached at the end of the email)
>
> Any ideas? The only thing I can think of, is the huge number of org. units
> that this instance has (42.000 org. units) with 8 GB. Would it be related
> to a memory problem? (although the XML file is very small)
>
> I have also selected Preloaded Cache = No
>
> Many thanks!
>
>
> *Error 1*
>
> * INFO  2016-10-13 21:55:55,780 [Level: INFO, category: DATAVALUE_IMPORT,
> time: Thu Oct 13 21:55:55 UTC 2016, message: Importing data values]
> (InMemoryNotifier.java [taskScheduler-7])
> * ERROR 2016-10-13 22:10:55,332 java.lang.RuntimeException:
> org.hibernate.PropertyAccessException: Exception occurred inside getter of
> org.hisp.dhis.organisationunit.OrganisationUnit.path
>         at
> org.hisp.dhis.commons.collection.CachingMap.get(CachingMap.java:90)
>         at
> org.hisp.dhis.dxf2.datavalueset.DefaultDataValueSetService.saveDataValueSet(DefaultDataValueSetService.java:954)
>         at
> org.hisp.dhis.dxf2.datavalueset.DefaultDataValueSetService.saveDataValueSet(DefaultDataValueSetService.java:488)
>         at
> org.hisp.dhis.dxf2.datavalueset.tasks.ImportDataValueTask.call(ImportDataValueTask.java:102)
>         at
> org.hisp.dhis.security.SecurityContextRunnable.run(SecurityContextRunnable.java:57)
>         at
> org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:54)
>         at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:266)
>         at
> java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
>         at
> java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
>         at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>         at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>         at java.lang.Thread.run(Thread.java:745)
> Caused by: org.hibernate.PropertyAccessException: Exception occurred
> inside getter of org.hisp.dhis.organisationunit.OrganisationUnit.path
>         at
> org.hibernate.property.access.spi.GetterMethodImpl.get(GetterMethodImpl.java:44)
>         at
> org.hibernate.tuple.entity.AbstractEntityTuplizer.getPropertyValues(AbstractEntityTuplizer.java:505)
>         at
> org.hibernate.tuple.entity.PojoEntityTuplizer.getPropertyValues(PojoEntityTuplizer.java:217)
>         at
> org.hibernate.persister.entity.AbstractEntityPersister.getPropertyValues(AbstractEntityPersister.java:4613)
>         at
> org.hibernate.event.internal.DefaultFlushEntityEventListener.getValues(DefaultFlushEntityEventListener.java:178)
>         at
> org.hibernate.event.internal.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:135)
>         at
> org.hibernate.event.internal.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:216)
>         at
> org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:85)
>         at
> org.hibernate.event.internal.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:44)
>         at
> org.hibernate.internal.SessionImpl.autoFlushIfRequired(SessionImpl.java:1264)
>         at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1780)
>         at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:363)
>         at
> org.hibernate.internal.CriteriaImpl.uniqueResult(CriteriaImpl.java:385)
>         at
> org.hisp.dhis.dataset.hibernate.HibernateLockExceptionStore.getCount(HibernateLockExceptionStore.java:167)
>         at
> org.hisp.dhis.dataset.DefaultDataSetService.isLockedPeriod(DefaultDataSetService.java:384)
>         at sun.reflect.GeneratedMethodAccessor709.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:498)
>         at
> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
>         at
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
>         at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
>         at
> org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
>         at
> org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
>         at
> org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
>         at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
>         at
> org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
>         at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
>         at
> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
>         at com.sun.proxy.$Proxy77.isLockedPeriod(Unknown Source)
>         at
> org.hisp.dhis.dxf2.datavalueset.DefaultDataValueSetService.lambda$saveDataValueSet$14(DefaultDataValueSetService.java:955)
>         at
> org.hisp.dhis.commons.collection.CachingMap.get(CachingMap.java:82)
>         ... 12 more
> Caused by: java.lang.reflect.InvocationTargetException
>         at sun.reflect.GeneratedMethodAccessor391.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:498)
>         at
> org.hibernate.property.access.spi.GetterMethodImpl.get(GetterMethodImpl.java:41)
>         ... 42 more
> Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
>         at
> java.lang.AbstractStringBuilder.<init>(AbstractStringBuilder.java:68)
>         at java.lang.StringBuilder.<init>(StringBuilder.java:101)
>         at org.apache.commons.lang3.StringUtils.join(StringUtils.java:4121)
>         at org.apache.commons.lang3.StringUtils.join(StringUtils.java:4177)
>         at
> org.hisp.dhis.organisationunit.OrganisationUnit.getPath(OrganisationUnit.java:901)
>         at sun.reflect.GeneratedMethodAccessor391.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:498)
>         at
> org.hibernate.property.access.spi.GetterMethodImpl.get(GetterMethodImpl.java:41)
>         at
> org.hibernate.tuple.entity.AbstractEntityTuplizer.getPropertyValues(AbstractEntityTuplizer.java:505)
>         at
> org.hibernate.tuple.entity.PojoEntityTuplizer.getPropertyValues(PojoEntityTuplizer.java:217)
>         at
> org.hibernate.persister.entity.AbstractEntityPersister.getPropertyValues(AbstractEntityPersister.java:4613)
>         at
> org.hibernate.event.internal.DefaultFlushEntityEventListener.getValues(DefaultFlushEntityEventListener.java:178)
>         at
> org.hibernate.event.internal.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:135)
>         at
> org.hibernate.event.internal.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:216)
>         at
> org.hibernate.event.internal.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:85)
>         at
> org.hibernate.event.internal.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:44)
>         at
> org.hibernate.internal.SessionImpl.autoFlushIfRequired(SessionImpl.java:1264)
>         at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1780)
>         at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:363)
>         at
> org.hibernate.internal.CriteriaImpl.uniqueResult(CriteriaImpl.java:385)
>         at
> org.hisp.dhis.dataset.hibernate.HibernateLockExceptionStore.getCount(HibernateLockExceptionStore.java:167)
>         at
> org.hisp.dhis.dataset.DefaultDataSetService.isLockedPeriod(DefaultDataSetService.java:384)
>         at sun.reflect.GeneratedMethodAccessor709.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:498)
>         at
> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302)
>         at
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
>         at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
>         at
> org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
>         at
> org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281)
>         at
> org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
>  (DefaultDataValueSetService.java [taskScheduler-3])
>
>
> -------------------------------------------------------------------------------------------------------------
>
>
> *Error 2:*
>
> * INFO  2016-10-13 22:47:36,040 [Level: INFO, category: DATAVALUE_IMPORT,
> time: Thu Oct 13 22:47:36 UTC 2016, message: Importing data values]
> (InMemoryNotifier.java [taskScheduler-7])
> CachingMap* INFO  2016-10-13 22:49:58,444 Org unit cache heated after
> cache miss threshold reached (DefaultDataValueSetService.java
> [taskScheduler-7])
> Org unit cache heated after cache miss threshold reached* ERROR 2016-10-13
> 22:56:14,899 Unable to render Velocity Template, '/main.vm'
> (CommonsLogger.java [http-apr-8081-exec-1])
> ClientAbortException:  java.io.IOException
>         at
> org.apache.catalina.connector.OutputBuffer.doFlush(OutputBuffer.java:371)
>         at
> org.apache.catalina.connector.OutputBuffer.flush(OutputBuffer.java:333)
>         at
> org.apache.catalina.connector.CoyoteOutputStream.flush(CoyoteOutputStream.java:101)
>         at
> org.springframework.security.web.context.OnCommittedResponseWrapper$SaveContextServletOutputStream.flush(OnCommittedResponseWrapper.java:437)
>         at sun.nio.cs.StreamEncoder.implFlush(StreamEncoder.java:297)
>         at sun.nio.cs.StreamEncoder.flush(StreamEncoder.java:141)
>         at java.io.OutputStreamWriter.flush(OutputStreamWriter.java:229)
>         at
> org.apache.struts2.dispatcher.VelocityResult.doExecute(VelocityResult.java:160)
>         at
> org.apache.struts2.dispatcher.StrutsResultSupport.execute(StrutsResultSupport.java:191)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.executeResult(DefaultActionInvocation.java:369)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:273)
>         at
> org.hisp.dhis.webportal.interceptor.XWorkPortalUserInterceptor.intercept(XWorkPortalUserInterceptor.java:85)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.hisp.dhis.webportal.interceptor.XWorkPortalModuleInterceptor.intercept(XWorkPortalModuleInterceptor.java:91)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.hisp.dhis.webportal.interceptor.XWorkPortalMenuInterceptor.intercept(XWorkPortalMenuInterceptor.java:94)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.hisp.dhis.webportal.interceptor.XWorkPortalParamsInterceptor.intercept(XWorkPortalParamsInterceptor.java:150)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.hisp.dhis.interceptor.ContextInterceptor.intercept(ContextInterceptor.java:83)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.hisp.dhis.interceptor.UserSettingInterceptor.intercept(UserSettingInterceptor.java:81)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.hisp.dhis.security.intercept.LoginInterceptor.intercept(LoginInterceptor.java:85)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at org.hisp.dhis.security.intercept.XWorkSecurityInterceptor.in
> tercept(XWorkSecurityInterceptor.java:116)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.hisp.dhis.interceptor.SystemSettingInterceptor.intercept(SystemSettingInterceptor.java:115)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.hisp.dhis.interceptor.I18nInterceptor.intercept(I18nInterceptor.java:139)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at com.opensymphony.xwork2.interceptor.ParametersInterceptor.do
> Intercept(ParametersInterceptor.java:229)
>         at
> com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercept(StaticParametersInterceptor.java:191)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.hisp.dhis.interceptor.ExceptionInterceptor.intercept(ExceptionInterceptor.java:113)
>         at
> com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:244)
>         at
> org.apache.struts2.impl.StrutsActionProxy.execute(StrutsActionProxy.java:54)
>         at
> org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:564)
>         at
> org.apache.struts2.dispatcher.ng.ExecuteOperations.executeAction(ExecuteOperations.java:81)
>         at
> org.apache.struts2.dispatcher.ng.filter.StrutsPrepareAndExecuteFilter.doFilter(StrutsPrepareAndExecuteFilter.java:99)
>         at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>         at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>         at
> org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
>         at
> org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
>         at
> org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
>
>
> _______________________________________________
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> More help   : https://help.launchpad.net/ListHelp
>
>
>
>
> --
> Lars Helge Øverland
> Lead developer, DHIS 2
> University of Oslo
> Skype: larshelgeoverland
> lars@xxxxxxxxx
> http://www.dhis2.org <https://www.dhis2.org/>
>
>
> _______________________________________________
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>