Getting below error if i try to save the data in MYSql DB in spring batch .
Caused by: org.springframework.dao.InvalidDataAccessApiUsageException: no transaction is in progress; nested exception is javax.persistence.TransactionRequiredException: no transaction is in progress
at org.springframework.orm.jpa.EntityManagerFactoryUtils.convertJpaAccessExceptionIfPossible(EntityManagerFactoryUtils.java:403) ~[spring-orm-5.2.3.RELEASE.jar:5.2.3.RELEASE]
at org.springframework.orm.jpa.vendor.HibernateJpaDialect.translateExceptionIfPossible(HibernateJpaDialect.java:257) ~[spring-orm-5.2.3.RELEASE.jar:5.2.3.RELEASE]
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:528) ~[spring-orm-5.2.3.RELEASE.jar:5.2.3.RELEASE]
at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:61) ~[spring-tx-5.2.3.RELEASE.jar:5.2.3.RELEASE]
at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:242) ~[spring-tx-5.2.3.RELEASE.jar:5.2.3.RELEASE]
at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:153) ~[spring-tx-5.2.3.RELEASE.jar:5.2.3.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.
Related
I have a Spring Boot web application with Hibernate that is launching several threads concurrently to process some jobs in parallel using a queue policy. The application is failing randomly with this exception:
org.hibernate.PessimisticLockException: could not execute statement
The most frecuent point where the application is failing is when a JPARepository tries to save an entity. I suppose it is trying to write it, but other thread has locked the same record before to read it. How can I get and debug which is the other process that is locking the row or table?. How can I get the locked rows to analyze the root cause? It is very difficult to me to debug and detect the problem, so I am a little bit lost and any help will be welcome.
The log stacktrace is at the end of these question.
This is my system configuration with MySQL 5 and these jars:
hibernate-c3p0-5.4.23.Final.jar
hibernate-commons-annotations-5.1.2.Final.jar
hibernate-core-5.4.23.Final.jar HikariCP-3.4.5.jar
mysql-connector-java-8.0.22.jar spring-boot-2.4.0.jar
spring-boot-starter-data-jpa-2.4.0.jar
spring-boot-starter-jdbc-2.4.0.jar spring-core-5.3.1.jar
spring-data-commons-2.4.1.jar
spring-data-commons-core-1.0.0.RELEASE.jar spring-data-jpa-2.4.1.jar
spring-jdbc-5.3.1.jar
And the stack trace:
[2022-01-04][09:10:45][ERROR][Thread-14] SqlExceptionHelper - Lock
wait timeout exceeded; try restarting transaction
[2022-01-04][09:10:45][ERROR][Thread-14] LocalStatusUpdater - [...]
could not execute statement; SQL [n/a]; nested exception is
org.hibernate.PessimisticLockException: could not execute statement
org.springframework.dao.PessimisticLockingFailureException: could not
execute statement; SQL [n/a]; nested exception is
org.hibernate.PessimisticLockException: could not execute statement
at
org.springframework.orm.jpa.vendor.HibernateJpaDialect.convertHibernateAccessException(HibernateJpaDialect.java:271)
at
org.springframework.orm.jpa.vendor.HibernateJpaDialect.translateExceptionIfPossible(HibernateJpaDialect.java:233)
at
org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:548)
at
org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:61)
at
org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:242)
at
org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:152)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.data.jpa.repository.support.CrudMethodMetadataPostProcessor$CrudMethodMetadataPopulatingMethodInterceptor.invoke(CrudMethodMetadataPostProcessor.java:174)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:97)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:215)
at com.sun.proxy.$Proxy145.save(Unknown Source) at com. [...] at
org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)
at
org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:771)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at
org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)
at
org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:371)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:134)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)
at
org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:691)
at com. [...] at
org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)
at
org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:771)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at
org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)
at
org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:371)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:134)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)
at
org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:691)
at com. [...] at
org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)
at
org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:771)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at
org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)
at
org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:371)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:134)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749)
at
org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:691)
at com. [...] at
org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)
at
org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:687)
at com. [...] at
org.springframework.security.concurrent.DelegatingSecurityContextRunnable.run(DelegatingSecurityContextRunnable.java:82)
at java.lang.Thread.run(Thread.java:748) Caused by:
org.hibernate.PessimisticLockException: could not execute statement
at
org.hibernate.dialect.MySQLDialect$3.convert(MySQLDialect.java:537)
at
org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113)
at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:99)
at
org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:200)
at
org.hibernate.dialect.identity.GetGeneratedKeysDelegate.executeAndExtract(GetGeneratedKeysDelegate.java:57)
at
org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:43)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3152)
at
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3758)
at
org.hibernate.action.internal.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:84)
at org.hibernate.engine.spi.ActionQueue.execute(ActionQueue.java:645)
at
org.hibernate.engine.spi.ActionQueue.addResolvedEntityInsertAction(ActionQueue.java:282)
at
org.hibernate.engine.spi.ActionQueue.addInsertAction(ActionQueue.java:263)
at
org.hibernate.engine.spi.ActionQueue.addAction(ActionQueue.java:317)
at
org.hibernate.event.internal.AbstractSaveEventListener.addInsertAction(AbstractSaveEventListener.java:330)
at
org.hibernate.event.internal.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:287)
at
org.hibernate.event.internal.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:193)
at
org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:123)
at
org.hibernate.event.internal.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:185)
at
org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:128)
at
org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:55)
at
org.hibernate.event.service.internal.EventListenerGroupImpl.fireEventOnEachListener(EventListenerGroupImpl.java:102)
at
org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:720)
at org.hibernate.internal.SessionImpl.persist(SessionImpl.java:706)
at sun.reflect.GeneratedMethodAccessor306.invoke(Unknown Source) at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498) at
org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:311)
at com.sun.proxy.$Proxy117.persist(Unknown Source) at
org.springframework.data.jpa.repository.support.SimpleJpaRepository.save(SimpleJpaRepository.java:557)
at sun.reflect.GeneratedMethodAccessor304.invoke(Unknown Source) at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498) at
org.springframework.data.repository.core.support.RepositoryMethodInvoker$RepositoryFragmentMethodInvoker.lambda$new$0(RepositoryMethodInvoker.java:289)
at
org.springframework.data.repository.core.support.RepositoryMethodInvoker.doInvoke(RepositoryMethodInvoker.java:137)
at
org.springframework.data.repository.core.support.RepositoryMethodInvoker.invoke(RepositoryMethodInvoker.java:121)
at
org.springframework.data.repository.core.support.RepositoryComposition$RepositoryFragments.invoke(RepositoryComposition.java:524)
at
org.springframework.data.repository.core.support.RepositoryComposition.invoke(RepositoryComposition.java:285)
at
org.springframework.data.repository.core.support.RepositoryFactorySupport$ImplementationMethodExecutionInterceptor.invoke(RepositoryFactorySupport.java:531)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.data.repository.core.support.QueryExecutorMethodInterceptor.doInvoke(QueryExecutorMethodInterceptor.java:156)
at
org.springframework.data.repository.core.support.QueryExecutorMethodInterceptor.invoke(QueryExecutorMethodInterceptor.java:131)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.data.projection.DefaultMethodInvokingMethodInterceptor.invoke(DefaultMethodInvokingMethodInterceptor.java:80)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:371)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:134)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:137)
... 58 common frames omitted Caused by:
com.mysql.cj.jdbc.exceptions.MySQLTransactionRollbackException: Lock
wait timeout exceeded; try restarting transaction at
com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:123)
at
com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:97)
at
com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:122)
at
com.mysql.cj.jdbc.ClientPreparedStatement.executeInternal(ClientPreparedStatement.java:953)
at
com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1092)
at
com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdateInternal(ClientPreparedStatement.java:1040)
at
com.mysql.cj.jdbc.ClientPreparedStatement.executeLargeUpdate(ClientPreparedStatement.java:1347)
at
com.mysql.cj.jdbc.ClientPreparedStatement.executeUpdate(ClientPreparedStatement.java:1025)
at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:1502)
at
org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:197)
... 102 common frames omitted
I am using springboot to connect to a mysql database. Please find my configuration below
spring.datasource.url=jdbc:<connection-url>
spring.datasource.username=<username>
spring.datasource.password=<password>
spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver
spring.jpa.show-sql=true
spring.jpa.hibernate.ddl-auto=update
spring.jpa.properties.hibernate.format_sql=true
spring.datasource.tomcat.max-active=50
spring.datasource.tomcat.max-idle=20
spring.datasource.tomcat.max-wait=20000
spring.datasource.tomcat.min-idle=15
Api code
#CrossOrigin(origins = "*", allowedHeaders = "*")
#GetMapping(value = "/validateuser/{consumerName}")
#Transactional
public Boolean valiadateuser(#PathVariable String consumerName) {
LOGGER.info("Inside validateuser -1");
ConsumerName user = consumerRepository.findByName(consumerName);
LOGGER.info("Inside validateuser -2 :::: " + user);
if (user != null) {
return Boolean.TRUE;
}
return Boolean.FALSE;
}
Below is my exception
org.springframework.orm.jpa.JpaSystemException: Unable to commit against JDBC Connection; nested exception is org.hibernate.TransactionException: Unable to commit against JDBC Connection
at org.springframework.orm.jpa.vendor.HibernateJpaDialect.convertHibernateAccessException(HibernateJpaDialect.java:353) ~[spring-orm-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.orm.jpa.vendor.HibernateJpaDialect.translateExceptionIfPossible(HibernateJpaDialect.java:255) ~[spring-orm-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.orm.jpa.JpaTransactionManager.doCommit(JpaTransactionManager.java:538) ~[spring-orm-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:743) [spring-tx-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:711) [spring-tx-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.completeTransactionAfterThrowing(TransactionAspectSupport.java:665) [spring-tx-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:370) [spring-tx-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) [spring-tx-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) [spring-aop-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:749) [spring-aop-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:691) [spring-aop-5.2.5.RELEASE.jar!/:5.2.5.RELEASE]
at com.server.controller.SubscribeController$$EnhancerBySpringCGLIB$$14f090fd.subscribeTopic(<generated>) [classes!/:0.0.1-SNAPSHOT]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_251]
Got the answer
updated the resource.properties
spring.datasource.url=jdbc:<connection-url>
spring.datasource.username=<username>
spring.datasource.password=<password>
#spring.datasource.driver-class-name=com.mysql.cj.jdbc.Driver
spring.jpa.show-sql=true
spring.jpa.hibernate.ddl-auto=update
spring.datasource.hikari.connectionTimeout=20000
spring.datasource.hikari.maximumPoolSize=5
I was experiencing the same exception on my Spring / Postgres stack. Basically, the DB can not return/commit all the rows that match your query in time.
It can be fixed by creating indexes on the columns used in the particular query. This speeds the query up.
CREATE INDEX index_redflag_person
ON redflag_person (firstname, alias,lastname,address,birthplace);
I use Spring and Hibernate and PostgreSQL for practice, got the similar exception:
org.springframework.transaction.TransactionSystemException: Could not commit Hibernate transaction;
nested exception is org.hibernate.TransactionException:
Unable to commit against JDBC Connection] with root cause
org.postgresql.util.PSQLException: Cannot commit when autoCommit is enabled.
my hibernate.prop has some config below
hibernate.dialect=org.hibernate.dialect.PostgreSQL10Dialect
hibernate.connection.handling_mode=DELAYED_ACQUISITION_AND_RELEASE_AFTER_STATEMENT
packages.to.scan=org.practice.dao.entity
It's weird bcs the default hibernate.connection.autocommit value in hibernate 5.6 is false
After a whole day search, I could not find the same error on the internet, finally I figured it out: somehow I added hibernate.connection.handling_mode in my config file, remove it(the default is fine) and the app works as expected
so maybe check the config and use the simplest param would help someone else
I have two pure Java EE applications, RemoteApp and ClientApp. I want to use ClientApp to access RemoteApp through a remote EJB to perfom some persistent action. I using JTA and CMT but when invoke anyone RemoteApp method in a Persistence Context and perform some Database action, the server simply does not respond until a transaction timeOut occurs.
To materialize what I said, I'll show the core code:
RemoteApp code:
package br.com;
#Remote
interface IRemote {void method();}
#Stateless
//I explained the use of these below annotations only for clarity
#TransactionManagement(value = TransactionManagementType.CONTAINER)
#TransactionAttribute(value = TransactionAttributeType.REQUIRED)
class Remote implements IRemote {
#PersistenceContext
private EntityManager em;
void method(){
em.persist(new MyEntity()); //A simple action just to example a Persistence Context situation
}
Persistence.xml of RemoteApp:
<persistence-unit name="remoteAppPU" transaction-type="JTA">
<jta-data-source>jdbc/remoteAppDS</jta-data-source>
<properties>
<property name="javax.persistence.jdbc.driver" value="com.mysql.jdbc.jdbc2.optional.MysqlXADataSource" />
<property name="eclipselink.ddl-generation.table-creation-suffix" value="engine=InnoDB"/>
</properties>
</persistence-unit>
Datasource of Glassfish domain of RemoteApp (config.xml):
<jdbc-connection-pool datasource-classname="com.mysql.jdbc.jdbc2.optional.MysqlXADataSource" name="remoteAppPool" res-type="javax.sql.XADataSource">
<property name="user" value="user"></property>
<property name="url" value="jdbc:mysql://remoteApp:3306/remoteAppDB"></property>
<property name="password" value="password"></property>
</jdbc-connection-pool>
<jdbc-resource pool-name="remoteAppPool" jndi-name="jdbc/remoteAppDS"></jdbc-resource>
Client-App code:
#Stateless
class LocalBean {
#EJB(mappedName = "corbaname:iiop:server.com:3700#java:global/RemoteApp/Remote!br.com.IRemote"
private IRemote remote;
#TransactionAttribute
void testMethod(){remote.method();}
}
When ClientApp invokes a RemoteApp method i got a exception after 30 minutes (I can't found a way to decrease this time):
javax.ejb.EJBException: Unable to complete container-managed transaction.
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:734)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:507)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4600)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2108)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2078)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
at com.sun.proxy.$Proxy283.testar(Unknown Source)
at br.com.ejb.EJB31_Generated__LocalBean__Intf____Bean.method(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:76)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:148)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:191)
at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:243)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:103)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:493)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:415)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:104)
at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:277)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:272)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:268)
at org.glassfish.jersey.internal.Errors.process(Errors.java:316)
at org.glassfish.jersey.internal.Errors.process(Errors.java:298)
at org.glassfish.jersey.internal.Errors.process(Errors.java:268)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:289)
at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:256)
at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:703)
at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:416)
at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:370)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:389)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:342)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:229)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1580)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:258)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:652)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:591)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:155)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:371)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:238)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:463)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:168)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:206)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:180)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:242)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:539)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:593)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:573)
at java.lang.Thread.run(Thread.java:748)
Caused by: javax.transaction.SystemException: org.omg.CORBA.UNKNOWN: ----------BEGIN server-side stack trace----------
org.omg.CORBA.UNKNOWN: ADVERTÊNCIA: 00010002: Unknown user exception thrown by the server - exception: javax.persistence.PersistenceException; message: Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.7.0.v20170811-d680af5): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: java.sql.SQLException: Error in allocating a connection. Cause: org.omg.CORBA.COMM_FAILURE: ADVERTÊNCIA: 00410019: Communications timeout waiting for response. Exceeded 1.800.000 milliseconds vmcid: OMG minor code: 19 completed: Maybe
Error Code: 0
Call: INSERT INTO MYENTITY (NAME) VALUES (?)
bind => [bla]
Query: InsertObjectQuery(br.com.MyEntity#0) vmcid: OMG minor code: 2 completed: Maybe
at com.sun.proxy.$Proxy194.runtimeexception(Unknown Source)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.convertThrowableToSystemException(MessageMediatorImpl.java:1764)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleThrowableDuringServerDispatch(MessageMediatorImpl.java:1714)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleThrowableDuringServerDispatch(MessageMediatorImpl.java:1679)
at com.sun.corba.ee.impl.protocol.ServerRequestDispatcherImpl.dispatch(ServerRequestDispatcherImpl.java:255)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleRequestRequest(MessageMediatorImpl.java:1550)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleRequest(MessageMediatorImpl.java:1426)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleInput(MessageMediatorImpl.java:931)
at com.sun.corba.ee.impl.protocol.giopmsgheaders.RequestMessage_1_2.callback(RequestMessage_1_2.java:213)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.handleRequest(MessageMediatorImpl.java:695)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.dispatch(MessageMediatorImpl.java:497)
at com.sun.corba.ee.impl.protocol.MessageMediatorImpl.doWork(MessageMediatorImpl.java:2223)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.performWork(ThreadPoolImpl.java:497)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.run(ThreadPoolImpl.java:540)
Caused by: javax.persistence.PersistenceException: Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.7.0.v20170811-d680af5): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: java.sql.SQLException: Error in allocating a connection. Cause: org.omg.CORBA.COMM_FAILURE: ADVERTÊNCIA: 00410019: Communications timeout waiting for response. Exceeded 1.800.000 milliseconds vmcid: OMG minor code: 19 completed: Maybe
Error Code: 0
Call: INSERT INTO MYENTITY (NAME) VALUES (?)
bind => [bla]
Query: InsertObjectQuery(br.com.MyEntity#0)
at org.eclipse.persistence.internal.jpa.EntityManagerSetupImpl$1.handleException(EntityManagerSetupImpl.java:772)
at org.eclipse.persistence.transaction.AbstractSynchronizationListener.handleException(AbstractSynchronizationListener.java:275)
at org.eclipse.persistence.transaction.AbstractSynchronizationListener.beforeCompletion(AbstractSynchronizationListener.java:170)
at org.eclipse.persistence.transaction.JTASynchronizationListener.beforeCompletion(JTASynchronizationListener.java:68)
at com.sun.jts.jta.SynchronizationImpl.before_completion(SynchronizationImpl.java:99)
at com.sun.jts.CosTransactions.RegisteredSyncs.distributeBefore(RegisteredSyncs.java:141)
at com.sun.jts.CosTransactions.TopCoordinator.beforeCompletion(TopCoordinator.java:2548)
at com.sun.jts.CosTransactions.CoordinatorSynchronizationImpl.before_completion(CoordinatorSynchronizationImpl.java:165)
at org.omg.CosTransactions.SynchronizationPOA._invoke(SynchronizationPOA.java:39)
at com.sun.corba.ee.impl.protocol.ServerRequestDispatcherImpl.dispatchToServant(ServerRequestDispatcherImpl.java:528)
at com.sun.corba.ee.impl.protocol.ServerRequestDispatcherImpl.dispatch(ServerRequestDispatcherImpl.java:199)
... 9 more
Caused by: Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.7.0.v20170811-d680af5): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: java.sql.SQLException: Error in allocating a connection. Cause: org.omg.CORBA.COMM_FAILURE: ADVERTÊNCIA: 00410019: Communications timeout waiting for response. Exceeded 1.800.000 milliseconds vmcid: OMG minor code: 19 completed: Maybe
Error Code: 0
Call: INSERT INTO MYENTITY (NAME) VALUES (?)
bind => [bla]
Query: InsertObjectQuery(br.com.MyEntity#0)
... repeated log
Here are some observations:
Both Apps are in different containers and security configs are disable.
I have been used Glassfish Server 5.0 with Java EE Specification 8.0
I have ben used mysql 5.7 with XA Protocol and engine InnoDB on tables
If I don't use a Persistence Context / persistent operation it works
If I use BMT it works
I'm insisting on this approach because i want to control transaction by client, otherwise I would use a SIMPLE web service
CMT = Container Management Transaction = TransactionManagementType.CONTAINER
BMT = Bean Management Transaction = TransactionManagementType.BEAN
What I think is causing the problem:
I suspect MySql is crashing in commit / rollback (But i was tried with Derby and same problem happened)
A problem with XA MySql DataSource
MySql transaction support. I suspected that InnoDB engine would solve... I was wrong.
I have a Java application running on successfully on Amazon Web Services Elastic Beanstalk.
I am trying to set up MySQL. I have created a DB Instance as you can see:
Question 1:
How do I connect my Java App to the Database?
I have the following code (after viewing this):
#Bean
public DataSource dataSource() {
// Openshift
// String host = System.getenv("OPENSHIFT_MYSQL_DB_HOST");
// String port = System.getenv("OPENSHIFT_MYSQL_DB_PORT");
// String username = System.getenv("OPENSHIFT_MYSQL_DB_USERNAME");
// String password = System.getenv("OPENSHIFT_MYSQL_DB_PASSWORD");
// AWS
String host = System.getenv("RDS_HOSTNAME");
String port = System.getenv("RDS_PORT");
String username = System.getenv("RDS_USERNAME");
String password = System.getenv("RDS_PASSWORD");
String dbname = System.getenv("RDS_DB_NAME");
DriverManagerDataSource dataSource = new DriverManagerDataSource();
dataSource.setDriverClassName(environment.getRequiredProperty("jdbc.driverClassName"));
if (host == null) {
dataSource.setUrl(environment.getRequiredProperty("jdbc.url"));
dataSource.setUsername(environment.getRequiredProperty("jdbc.username"));
dataSource.setPassword(environment.getRequiredProperty("jdbc.password"));
} else {
//dataSource.setUrl("jdbc:mysql://" + host + ":" + port + "/");
// Openshift
//dataSource.setUrl("jdbc:mysql://" + host + ":" + port + "/" + environment.getRequiredProperty("jdbc.dbname"));
// AWS
dataSource.setUrl("jdbc:mysql://" + host + ":" + port + "/" + dbname);
dataSource.setUsername(username);
dataSource.setPassword(password);
System.out.println("jdbc:mysql://" + host + ":" + port + "/" + dbname+", username: "+username+", password: "+password);
}
return dataSource;
}
(p.s. the commented out code works on OpenShifts server)
But I get the following:
org.springframework.web.util.NestedServletException: Request
processing failed; nested exception is
org.springframework.transaction.CannotCreateTransactionException:
Could not open JPA EntityManager for transaction; nested exception is
org.hibernate.exception.JDBCConnectionException: Unable to acquire
JDBC Connection
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:982)
Question 2:
From an existing database, in MySQL Workbench, I have exported sql scripts to create a schema and tables, and then populate them. How do I import this into the AWS RDS MySQL database?
More info:
Server Logs:
-------------------------------------
/var/log/tomcat8/localhost.2017-02-21.log
-------------------------------------
21-Feb-2017 14:42:51.133 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log 1 Spring WebApplicationInitializers detected on classpath
21-Feb-2017 14:42:51.737 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Initializing Spring FrameworkServlet 'rest'
21-Feb-2017 14:57:36.680 SEVERE [http-nio-8080-exec-7] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [rest] in context with path [] threw exception [Request processing failed; nested exception is org.springframework.transaction.CannotCreateTransactionException: Could not open JPA EntityManager for transaction; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to acquire JDBC Connection] with root cause
java.net.ConnectException: Connection refused (Connection refused)
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at java.net.Socket.connect(Socket.java:538)
at java.net.Socket.<init>(Socket.java:434)
at java.net.Socket.<init>(Socket.java:244)
at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:258)
at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:306)
at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2504)
at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2541)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2323)
at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:832)
at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:408)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:417)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:344)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:208)
at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnectionFromDriverManager(DriverManagerDataSource.java:153)
at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnectionFromDriver(DriverManagerDataSource.java:144)
at org.springframework.jdbc.datasource.AbstractDriverBasedDataSource.getConnectionFromDriver(AbstractDriverBasedDataSource.java:155)
at org.springframework.jdbc.datasource.AbstractDriverBasedDataSource.getConnection(AbstractDriverBasedDataSource.java:120)
at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:122)
at org.hibernate.internal.NonContextualJdbcConnectionAccess.obtainConnection(NonContextualJdbcConnectionAccess.java:35)
at org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.acquireConnectionIfNeeded(LogicalConnectionManagedImpl.java:99)
at org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.getPhysicalConnection(LogicalConnectionManagedImpl.java:129)
at org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.getConnectionForTransactionManagement(LogicalConnectionManagedImpl.java:247)
at org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.begin(LogicalConnectionManagedImpl.java:254)
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl$TransactionDriverControlImpl.begin(JdbcResourceLocalTransactionCoordinatorImpl.java:203)
at org.hibernate.engine.transaction.internal.TransactionImpl.begin(TransactionImpl.java:56)
at org.springframework.orm.jpa.DefaultJpaDialect.beginTransaction(DefaultJpaDialect.java:67)
at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:380)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:373)
at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:427)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:276)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy55.findAll(Unknown Source)
at com.jobs.spring.controller.CategoryRESTService.findAllCategorys(CategoryRESTService.java:31)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:114)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:963)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:897)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:861)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:676)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:509)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1104)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1520)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1476)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
21-Feb-2017 15:09:21.090 INFO [localhost-startStop-2] org.apache.catalina.core.ApplicationContext.log Destroying Spring FrameworkServlet 'rest'
21-Feb-2017 15:09:38.729 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log 1 Spring WebApplicationInitializers detected on classpath
21-Feb-2017 15:09:39.329 INFO [localhost-startStop-1] org.apache.catalina.core.ApplicationContext.log Initializing Spring FrameworkServlet 'rest'
UPDATE
I also added rules to open it for everyone, but still get the same error:
The problem has to do with your database and the security group.
Hover to the "i" icon next to the Cluster Endpoint.
A popup will appear with the security groups.
Hit the first default link and you will be redirected to the security groups configuration.
Then you have to edit the security group and add an inbound rule in order to include your local ip.
Keep in mind that this will work only if your rds is on a public subnet.
This link is pretty helpful for troubleshooting.
More information on security groups
## when i submit my task to do some query from mysql to yarn by using spark's cluster mode like below: ##
./spark-submit --class org.com.scala.test.ScalaTestFile --master yarn --deploy-mode cluster --driver-memory 8g --executor-memory 5g --jars /usr/local/spark/lib/datanucleus-api-jdo-3.2.6.jar,/usr/local/spark/lib/datanucleus-core-3.2.10.jar,/usr/local/spark/lib/datanucleus-rdbms-3.2.9.jar,/usr/local/spark/lib/mysql-connector-java-5.1.26-bin.jar /data/tmp/snodawn/svn/scalaScript/scalaMavenTest/out/artifacts/scalaMavenTest_jar/scalaMavenTest.jar
- org.com.scala.test.ScalaTestFile is to query large amount of data in mysql(which for about 1 billion lines), and save it to hive :
val conf = new SparkConf().setAppName("ScalaTestFile")
val spark = new SparkContext(conf)
val sqlContext = new SQLContext(spark)
val hiveContext = new HiveContext(spark);
val reader = hiveContext.read.format("jdbc")
val url="jdbc:mysql://xx.xx.xx.xx:3307/databases"
reader.option("url",url)
reader.option("driver","com.mysql.jdbc.Driver")
reader.option("user","admin")
reader.option("password","admin")
reader.option("dbtable","(select * from gold) as a")
val df = reader.load()
val nTable = df.toDF();
val nWrite = nTable.write
hiveContext.sql("use testment")
nWrite.saveAsTable("gold_test")
- the task will be failed after running with such error:
16/02/24 18:46:43 INFO DAGScheduler: Job 0 failed: saveAsTable at ScalaTestFile.scala:88, took 1697.970350 s
16/02/24 18:46:43 ERROR InsertIntoHadoopFsRelation: Aborting job.
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1431)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1419)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1418)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1418)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:799)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:799)
at scala.Option.foreach(Option.scala:236)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:799)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1640)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1599)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1588)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:620)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1832)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1845)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1922)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation$$anonfun$run$1.apply$mcV$sp(InsertIntoHadoopFsRelation.scala:150)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation$$anonfun$run$1.apply(InsertIntoHadoopFsRelation.scala:108)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation$$anonfun$run$1.apply(InsertIntoHadoopFsRelation.scala:108)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:56)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation.run(InsertIntoHadoopFsRelation.scala:108)
at org.apache.spark.sql.execution.ExecutedCommand.sideEffectResult$lzycompute(commands.scala:58)
at org.apache.spark.sql.execution.ExecutedCommand.sideEffectResult(commands.scala:56)
at org.apache.spark.sql.execution.ExecutedCommand.doExecute(commands.scala:70)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$5.apply(SparkPlan.scala:132)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$5.apply(SparkPlan.scala:130)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:130)
at org.apache.spark.sql.execution.datasources.ResolvedDataSource$.apply(ResolvedDataSource.scala:256)
at org.apache.spark.sql.hive.execution.CreateMetastoreDataSourceAsSelect.run(commands.scala:258)
at org.apache.spark.sql.execution.ExecutedCommand.sideEffectResult$lzycompute(commands.scala:58)
at org.apache.spark.sql.execution.ExecutedCommand.sideEffectResult(commands.scala:56)
at org.apache.spark.sql.execution.ExecutedCommand.doExecute(commands.scala:70)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$5.apply(SparkPlan.scala:132)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$5.apply(SparkPlan.scala:130)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:130)
at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:55)
at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:55)
at org.apache.spark.sql.DataFrameWriter.saveAsTable(DataFrameWriter.scala:251)
at org.apache.spark.sql.DataFrameWriter.saveAsTable(DataFrameWriter.scala:221)
at org.com.scala.test.ScalaTestFile$.main(ScalaTestFile.scala:88)
at org.com.scala.test.ScalaTestFile.main(ScalaTestFile.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anon$2.run(ApplicationMaster.scala:542)
16/02/24 18:46:44 ERROR DefaultWriterContainer: Job job_201602241818_0000 aborted.
16/02/24 18:46:44 ERROR ApplicationMaster: User class threw exception: org.apache.spark.SparkException: Job aborted.
org.apache.spark.SparkException: Job aborted.
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation$$anonfun$run$1.apply$mcV$sp(InsertIntoHadoopFsRelation.scala:156)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation$$anonfun$run$1.apply(InsertIntoHadoopFsRelation.scala:108)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation$$anonfun$run$1.apply(InsertIntoHadoopFsRelation.scala:108)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:56)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation.run(InsertIntoHadoopFsRelation.scala:108)
at org.apache.spark.sql.execution.ExecutedCommand.sideEffectResult$lzycompute(commands.scala:58)
at org.apache.spark.sql.execution.ExecutedCommand.sideEffectResult(commands.scala:56)
at org.apache.spark.sql.execution.ExecutedCommand.doExecute(commands.scala:70)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$5.apply(SparkPlan.scala:132)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$5.apply(SparkPlan.scala:130)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:130)
at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:55)
at org.apache.spark.sql.hive.execution.CreateMetastoreDataSourceAsSelect.run(commands.scala:258)
at org.apache.spark.sql.execution.ExecutedCommand.sideEffectResult$lzycompute(commands.scala:58)
at org.apache.spark.sql.execution.ExecutedCommand.sideEffectResult(commands.scala:56)
at org.apache.spark.sql.execution.ExecutedCommand.doExecute(commands.scala:70)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$5.apply(SparkPlan.scala:132)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$5.apply(SparkPlan.scala:130)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:150)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:130)
at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:55)
at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:55)
at org.apache.spark.sql.DataFrameWriter.saveAsTable(DataFrameWriter.scala:251)
at org.apache.spark.sql.DataFrameWriter.saveAsTable(DataFrameWriter.scala:221)
at org.com.scala.test.ScalaTestFile$.main(ScalaTestFile.scala:88)
at org.com.scala.test.ScalaTestFile.main(ScalaTestFile.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anon$2.run(ApplicationMaster.scala:542)
Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 4 times, most recent failure: Lost task 0.3 in stage 0.0 (TID 3, slave4.4399data.com): ExecutorLos
tFailure (executor 4 exited caused by one of the running tasks) Reason: Executor heartbeat timed out after 122713 ms
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1431)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1419)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1418)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1418)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:799)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:799)
at scala.Option.foreach(Option.scala:236)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:799)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1640)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1599)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1588)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:620)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1832)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1845)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1922)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation$$anonfun$run$1.apply$mcV$sp(InsertIntoHadoopFsRelation.scala:150)
... 33 more
16/02/24 18:46:44 INFO ApplicationMaster: Final app status: FAILED, exitCode: 15, (reason: User class threw exception: org.apache.spark.SparkException: Job aborted.)
it seems that because it needs a log of time for querying from mysql and there returns no responses for a long time, this application finishes with failed status.
so, how can i solve my problem of querying from mysql for getting large amount of data by using spark?
ps, when i use java to do such query, i will do it like this:
Connection conn = DriverManager.getConnection(hiveConnectString, username, password);
com.mysql.jdbc.Statement statement = (com.mysql.jdbc.Statement)conn.createStatement();
statement.enableStreamingResults();
statement.executeUpdate("select * from gold")
so, is there a solution in spark to handling big data querying?