Seems like a memory issue java.lang.OutOfMemoryError: GC overhead limit exceeded
On Fri, Oct 14, 2016, 13:35 Jose Garcia Muñoz <[email protected]> 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 <[email protected]> > 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 <[email protected]> > 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) > > > _______________________________________________ > Mailing list: https://launchpad.net/~dhis2-devs > Post to : [email protected] > Unsubscribe : https://launchpad.net/~dhis2-devs > More help : https://help.launchpad.net/ListHelp > > > > > -- > Lars Helge Øverland > Lead developer, DHIS 2 > University of Oslo > Skype: larshelgeoverland > [email protected] > http://www.dhis2.org <https://www.dhis2.org/> > > > _______________________________________________ > Mailing list: https://launchpad.net/~dhis2-devs > Post to : [email protected] > Unsubscribe : https://launchpad.net/~dhis2-devs > More help : https://help.launchpad.net/ListHelp >
_______________________________________________ Mailing list: https://launchpad.net/~dhis2-devs Post to : [email protected] Unsubscribe : https://launchpad.net/~dhis2-devs More help : https://help.launchpad.net/ListHelp
