dhis2-devs team mailing list archive

[Jose Garcia Muñoz <josemp10@xxxxxxxxx>]

It seems to be memory issue happening in 2.24? If I try the same import
with the same org.units in 2.22, everything works well. With 2.24, I'm
normally getting the follow log message...

* INFO  2016-10-17 14:03:07,531 Org unit cache heated after cache miss
threshold reached (DefaultDataValueSetService.java [taskScheduler-6])


On Fri, Oct 14, 2016 at 1:51 PM, Jason Pickering <
jason.p.pickering@xxxxxxxxx> wrote:

> 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(DelegatingErrorHandlingRunnabl
>> e.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.DefaultFlushEntityEventListene
>> r.getValues(DefaultFlushEntityEventListener.java:178)
>>         at org.hibernate.event.internal.DefaultFlushEntityEventListene
>> r.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.DefaultFlushEntityEventListene
>> r.getValues(DefaultFlushEntityEventListener.java:178)
>>         at org.hibernate.event.internal.DefaultFlushEntityEventListene
>> r.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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>> 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
>> lars@xxxxxxxxx
>> http://www.dhis2.org <https://www.dhis2.org/>
>>
>>
>> _______________________________________________
>> Mailing list: https://launchpad.net/~dhis2-devs
>> Post to     : dhis2-devs@xxxxxxxxxxxxxxxxxxx
>> Unsubscribe : https://launchpad.net/~dhis2-devs
>> More help   : https://help.launchpad.net/ListHelp
>>
>