Spring Data JPA OutOfMemoryError: GC overhead limit exceeded

Question

I'm developing an application with huge size of entities(3072). We used jhipster for project structure. Everthing was ok so far until we want to upgrade Spring Boot version from 1.3.2 ( 1.9.2 spring-data-jpa ) to current 1.5.1 (spring-data-jpa 1.11.0) I'm getting following exception while startup. giving more memory, heap size etc. didnt help. i think problem is somehow related to spring-data-jpa after 1.10.X, because we dont have such problem in spring-data-jpa 1.9.x

    Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'ebysMesajTasfiyeJob': Unsatisfied dependency expressed through field 'messageService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'ebysMessageService': Unsatisfied dependency expressed through field 'saklamaPlaniService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'YEBYSaklamaPlaniService': Unsatisfied dependency expressed through field 'repository'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'YEBYSaklamaPlaniRepository': Cannot resolve reference to bean 'jpaMappingContext' while setting bean property 'mappingContext'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaMappingContext': Invocation of init method failed; nested exception is java.lang.OutOfMemoryError: GC overhead limit exceeded
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:588)
    at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88)
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:366)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1264)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:866)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:542)
    at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:122)
    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:737)
    at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:370)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:314)
    at org.springframework.boot.web.support.SpringBootServletInitializer.run(SpringBootServletInitializer.java:152)
    at org.springframework.boot.web.support.SpringBootServletInitializer.createRootApplicationContext(SpringBootServletInitializer.java:132)
    at org.springframework.boot.web.support.SpringBootServletInitializer.onStartup(SpringBootServletInitializer.java:87)
    at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5244)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
    ... 42 more
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'ebysMessageService': Unsatisfied dependency expressed through field 'saklamaPlaniService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'YEBYSaklamaPlaniService': Unsatisfied dependency expressed through field 'repository'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'YEBYSaklamaPlaniRepository': Cannot resolve reference to bean 'jpaMappingContext' while setting bean property 'mappingContext'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaMappingContext': Invocation of init method failed; nested exception is java.lang.OutOfMemoryError: GC overhead limit exceeded
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:588)
    at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88)
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:366)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1264)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
    at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:585)
    ... 64 more
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'YEBYSaklamaPlaniService': Unsatisfied dependency expressed through field 'repository'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'YEBYSaklamaPlaniRepository': Cannot resolve reference to bean 'jpaMappingContext' while setting bean property 'mappingContext'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaMappingContext': Invocation of init method failed; nested exception is java.lang.OutOfMemoryError: GC overhead limit exceeded
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:588)
    at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88)
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:366)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1264)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
    at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:585)
    ... 77 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'YEBYSaklamaPlaniRepository': Cannot resolve reference to bean 'jpaMappingContext' while setting bean property 'mappingContext'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaMappingContext': Invocation of init method failed; nested exception is java.lang.OutOfMemoryError: GC overhead limit exceeded
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:359)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1531)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1276)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
    at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:585)
    ... 90 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jpaMappingContext': Invocation of init method failed; nested exception is java.lang.OutOfMemoryError: GC overhead limit exceeded
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1628)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
    ... 103 more
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
    at java.util.HashMap.resize(HashMap.java:703)
    at java.util.HashMap.putVal(HashMap.java:662)
    at java.util.HashMap.put(HashMap.java:611)
    at java.util.HashSet.add(HashSet.java:219)
    at org.springframework.data.jpa.util.JpaMetamodel.getManagedTypes(JpaMetamodel.java:85)
    at org.springframework.data.jpa.util.JpaMetamodel.isJpaManaged(JpaMetamodel.java:61)
    at org.springframework.data.jpa.mapping.JpaPersistentPropertyImpl.isEntity(JpaPersistentPropertyImpl.java:159)
    at org.springframework.data.mapping.model.AbstractPersistentProperty.getPersistentEntityType(AbstractPersistentProperty.java:129)
    at org.springframework.data.jpa.mapping.JpaPersistentPropertyImpl.getPersistentEntityType(JpaPersistentPropertyImpl.java:133)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:507)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:465)
    at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:693)
    at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:329)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:508)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:465)
    at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:693)
    at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:329)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:508)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:465)
    at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:693)
    at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:329)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:508)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:465)
    at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:693)
    at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:329)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:508)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:465)
    at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:693)
    at org.springframework.data.mapping.context.AbstractMappingContext.addPersistentEntity(AbstractMappingContext.java:329)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.createAndRegisterProperty(AbstractMappingContext.java:508)
    at org.springframework.data.mapping.context.AbstractMappingContext$PersistentPropertyCreator.doWith(AbstractMappingContext.java:465)
    at org.springframework.util.ReflectionUtils.doWithFields(ReflectionUtils.java:693)

Hi, have you see this post: http://stackoverflow.com/a/1393503/2463802 ? — Marcos Nunes, Feb 15 '17 at 16:38
When you say 3072 entities, do you mean 3072 entity classes or instances? — Gaël Marziou, Feb 15 '17 at 19:06
@MarcosNunes thank you for given link. But we couldnt find problem. — Runomu, Feb 16 '17 at 06:22
Wow that's a lot for a monolith, current answers or comments focused on data volume (pagination) while it rather looks like an issue with Spring data/ hibernate when it builds its metadata from database at startup. Very unlikely a Jhipster issue. — Gaël Marziou, Feb 16 '17 at 09:17
@GaëlMarziou Yes its looks like an issue with Spring Data JPA/Data Commons after 1.10.X. Because as i said, we dont have any problem with 1.9.X spring-data-jpa. I'm still debugging desperately to find out problem. — Runomu, Feb 16 '17 at 17:13

score 3 · Answer 1 · answered Feb 15 '17 at 16:55

3

GC overhead limit exceeded means that your application has a lot of objects and the GC is spending most of the time collecting those objects. The usual way to solve this would be to take a heap dump and analyze those heap dump using a tool like Eclipse MAT.

From the logs, it seems that the application ran out of memory while putting a value to the HashMap.

You mentioned that you have a lot of entities in your application. Does that mean you are trying to load of data from database at once? In that case, why not modify your application to support pagination. That way, you don't load a lot of data in your application and might avoid this error.

answered Feb 15 '17 at 16:55

Rahul Sharma

5,562
4
24
48

thank you for your suggestion. we are not trying to load anything from DB while startup. spring data AbstractMappingContext trying to load these entities recursively and after a while application freezing for ca 10 mins. After ca 10 minutes we are getting exception given above. – Runomu Feb 16 '17 at 06:16
But its really interesting that we dont have any problem in spring boot 1.3.2( with spring-data-jpa 1.9.X) – Runomu Feb 16 '17 at 06:23

score 0 · Answer 2 · answered Dec 10 '18 at 11:38

Note that error "GC overhead limit exceeded" can also be caused by low xmx memory value. I had it on 64m and it ran smooth for some time, until i added a few extra jpa entities, which likely did put it over the edge.

I suspect that the startup process of jpa is quite memory intensive. Spend some time looking for recursive problems cause the cpu usage would be very high for minutes and sometimes the error would never appear and it would just be stuck.

score -1 · Answer 3 · answered Feb 27 '17 at 20:36

-1

If you are trying to solve a problem recursively forever (which it sounds like you are doing), you will eventually get a stack overflow. Try changing the recursive code to iterative.

answered Feb 27 '17 at 20:36

tezcan

9
1

Spring Data JPA OutOfMemoryError: GC overhead limit exceeded

3 Answers3