Develop Reference

Multi Threaded App With Issues Aquiring DB Connections

I have a Java application that reads data from a CSV file, turns them into business objects, and then saves them to a db. Most of the work is done single-threaded, but some of it is done using multiple threads. The application uses Spring framework, Hibernate as the ORM provider, c3p0 as the connection pool provider, and MySQL as the database. The parts of the application which are multi-threaded are annotated with #Async, using a ThreadPoolTaskExecutor created as a bean for the TaskExecutor that will do this work. The #Aysnc annotated methods return CompletableFuture.
With a small CSV file (under 10k records) everything is fine. However, some of our clients have much larger files (150k records) and this increase in load produces issues during the multi-threaded portions of the application. Here is one of the #Async annotated methods:
public class AppointmentTreeDAO {
#Autowired
private AppointmentRepository appointmentRepository;
private static final Logger logger = LoggerFactory.getLogger(AppointmentTreeDAO.class);
#Async
public CompletableFuture<Appointment> getObjectTree(Long oldApptId) {
logger.info("getting appointment thread");
return CompletableFuture.completedFuture(appointmentRepository.findByApptId(oldApptId));
}
}
This is the AppointmentRepository class (the last method is the one the code in question is calling):
public interface AppointmentRepository extends JpaRepository<Appointment, Long> {
List<Appointment> findByAccountId(String accountId);
List<Appointment> findByAccountIdAndProductIdAndApptStartDatetimeBetween(String accountId,
String productId, Date startDate, Date endDte);
Slice<Appointment> findByAccountIdAndProductIdAndApptStartDatetimeBetween(String accountId,
String productId, Date startDate, Date endDte, Pageable pageable);
#Query(value = "select a.appt_id from appointment a where a.appt_start_datetime " +
"between :startDate AND :endDate and a.account_id = :accountId and a.product_id = :productId",
nativeQuery = true)
List<Long> findByApptIdBetween(#Param("startDate") String startDate, #Param("endDate") String endDate,
#Param("accountId") String accountId, #Param("productId") String productId);
Appointment findByApptId(Long apptId);
}
Since I have that log line in the AppointmentTreeDAO class, I am able to see in the logs that each thread is doing work:
2:58:12.771 PM
2021-11-11 14:58:12.771 INFO 1 --- [mtSave-38] c.t.etl.repository.AppointmentTreeDAO : getting appointment thread
Eventually, I start seeing exceptions like this from the threads (same thread as above in this case):
2:58:16.790 PM
2021-11-11 14:58:16.790 WARN 1 --- [mtSave-38] o.h.engine.jdbc.spi.SqlExceptionHelper : SQL Error: 0, SQLState: 08001
2:58:16.803 PM
2021-11-11 14:58:16.803 ERROR 1 --- [mtSave-38] o.h.engine.jdbc.spi.SqlExceptionHelper : Could not create connection to database server. Attempted reconnect 3 times. Giving up.
2:58:16.804 PM
2021-11-11 14:58:16.804 WARN 1 --- [mtSave-38] c.t.etl.pipeline.load.Loader : java.util.concurrent.CompletionException: org.springframework.dao.DataAccessResourceFailureException: Unable to acquire JDBC Connection; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to acquire JDBC Connection
at org.springframework.aop.interceptor.AsyncExecutionAspectSupport.lambda$doSubmit$3(AsyncExecutionAspectSupport.java:279)
at java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1590)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.springframework.dao.DataAccessResourceFailureException: Unable to acquire JDBC Connection; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to acquire JDBC Connection
at org.springframework.orm.jpa.vendor.HibernateJpaDialect.convertHibernateAccessException(HibernateJpaDialect.java:255)
at org.springframework.orm.jpa.vendor.HibernateJpaDialect.translateExceptionIfPossible(HibernateJpaDialect.java:233)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:551)
at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:61)
at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:242)
at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:152)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.data.jpa.repository.support.CrudMethodMetadataPostProcessor$CrudMethodMetadataPopulatingMethodInterceptor.invoke(CrudMethodMetadataPostProcessor.java:145)
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.$Proxy148.findByApptId(Unknown Source)
at com.etl.repository.AppointmentTreeDAO.getObjectTree(AppointmentTreeDAO.java:25)
at com.etl.repository.AppointmentTreeDAO$$FastClassBySpringCGLIB$$fb95149d.invoke(<generated>)
at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218)
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:779)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750)
at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:137)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750)
at org.springframework.aop.interceptor.AsyncExecutionInterceptor.lambda$invoke$0(AsyncExecutionInterceptor.java:115)
at org.springframework.aop.interceptor.AsyncExecutionAspectSupport.lambda$doSubmit$3(AsyncExecutionAspectSupport.java:276)
... 4 more
Caused by: org.hibernate.exception.JDBCConnectionException: Unable to acquire JDBC Connection
at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:48)
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.resource.jdbc.internal.LogicalConnectionManagedImpl.acquireConnectionIfNeeded(LogicalConnectionManagedImpl.java:111)
at org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.getPhysicalConnection(LogicalConnectionManagedImpl.java:138)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.connection(StatementPreparerImpl.java:50)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:149)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:176)
at org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:151)
at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:2103)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:2040)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:2018)
at org.hibernate.loader.Loader.doQuery(Loader.java:948)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:349)
at org.hibernate.loader.Loader.doList(Loader.java:2849)
at org.hibernate.loader.Loader.doList(Loader.java:2831)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2663)
at org.hibernate.loader.Loader.list(Loader.java:2658)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:506)
at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:400)
at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:219)
at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1414)
at org.hibernate.query.internal.AbstractProducedQuery.doList(AbstractProducedQuery.java:1625)
at org.hibernate.query.internal.AbstractProducedQuery.list(AbstractProducedQuery.java:1593)
at org.hibernate.query.internal.AbstractProducedQuery.getSingleResult(AbstractProducedQuery.java:1641)
at org.hibernate.query.criteria.internal.compile.CriteriaQueryTypeQueryAdapter.getSingleResult(CriteriaQueryTypeQueryAdapter.java:111)
at org.springframework.data.jpa.repository.query.JpaQueryExecution$SingleEntityExecution.doExecute(JpaQueryExecution.java:196)
at org.springframework.data.jpa.repository.query.JpaQueryExecution.execute(JpaQueryExecution.java:88)
at org.springframework.data.jpa.repository.query.AbstractJpaQuery.doExecute(AbstractJpaQuery.java:155)
at org.springframework.data.jpa.repository.query.AbstractJpaQuery.execute(AbstractJpaQuery.java:143)
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.QueryExecutorMethodInterceptor.doInvoke(QueryExecutorMethodInterceptor.java:152)
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.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:137)
... 22 more
Caused by: java.sql.SQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:110)
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:97)
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:89)
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:63)
at com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:73)
at com.mysql.cj.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:903)
at com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:828)
at com.mysql.cj.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:453)
at com.mysql.cj.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:246)
at com.mysql.cj.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:198)
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:155)
at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnectionFromDriver(DriverManagerDataSource.java:146)
at org.springframework.jdbc.datasource.AbstractDriverBasedDataSource.getConnectionFromDriver(AbstractDriverBasedDataSource.java:205)
at org.springframework.jdbc.datasource.AbstractDriverBasedDataSource.getConnection(AbstractDriverBasedDataSource.java:169)
at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:122)
at org.hibernate.internal.NonContextualJdbcConnectionAccess.obtainConnection(NonContextualJdbcConnectionAccess.java:38)
at org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.acquireConnectionIfNeeded(LogicalConnectionManagedImpl.java:108)
... 60 more
Caused by: com.mysql.cj.exceptions.CJCommunicationsException: Communications link failure
The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
at sun.reflect.GeneratedConstructorAccessor129.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.cj.exceptions.ExceptionFactory.createException(ExceptionFactory.java:61)
at com.mysql.cj.exceptions.ExceptionFactory.createException(ExceptionFactory.java:105)
at com.mysql.cj.exceptions.ExceptionFactory.createException(ExceptionFactory.java:151)
at com.mysql.cj.exceptions.ExceptionFactory.createCommunicationsException(ExceptionFactory.java:167)
at com.mysql.cj.protocol.a.NativeSocketConnection.connect(NativeSocketConnection.java:89)
at com.mysql.cj.NativeSession.connect(NativeSession.java:144)
at com.mysql.cj.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:847)
... 73 more
Caused by: java.net.NoRouteToHostException: Cannot assign requested address (Address not available)
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 com.mysql.cj.protocol.StandardSocketFactory.connect(StandardSocketFactory.java:155)
at com.mysql.cj.protocol.a.NativeSocketConnection.connect(NativeSocketConnection.java:63)
... 75 more
2:58:16.804 PM
2021-11-11 14:58:16.804 WARN 1 --- [mtSave-38] c.t.etl.pipeline.load.Loader : Thread 77 ProcessFutures Loop Exception: org.springframework.dao.DataAccessResourceFailureException: Unable to acquire JDBC Connection;
nested exception is org.hibernate.exception.JDBCConnectionException: Unable to acquire JDBC Connection
Soon after throwing the above exception it starts doing work again and its now able to call the db when it couldn't just a short time ago:
2:58:16.807 PM
2021-11-11 14:58:16.807 INFO 1 --- [mtSave-38] c.t.etl.repository.AppointmentTreeDAO : getting appointment thread
This happens intermittently with many different threads, if not all. But eventually all the work is complete and all futures are returned from that method. Then the application returns to being single threaded and the exceptions stop. Once the application returns to using multiple threads the same exceptions as above occur again.
This is my persistence.xml file:
<properties>
<property name="javax.persistence.jdbc.driver" value="com.mysql.jdbc.Driver" />
<property name="hibernate.dialect" value="org.hibernate.dialect.MySQLDialect" />
<property name="hibernate.show_sql" value="false" />
<property name="hibernate.id.new_generator_mappings" value="false" />
<property name="org.hibernate.flushMode" value="ALWAYS" />
<property name="hibernate.c3p0.acquire_increment" value="1" />
<property name="hibernate.c3p0.idle_test_period" value="60"/>
<property name="hibernate.c3p0.max_size" value="54"/>
<property name="hibernate.c3p0.max_statements" value="50"/>
<property name="hibernate.c3p0.min_size" value="5"/>
</properties>
This is how the TaskExecutor is created:
public Executor taskExecutor() {
logger.info("Creating Async Task Executor");
final ThreadPoolTaskExecutor executor = new ThreadPoolTaskExecutor();
executor.setCorePoolSize(45);
executor.setMaxPoolSize(45);
executor.setThreadNamePrefix("mtSave-");
executor.initialize();
executor.setKeepAliveSeconds(120);
return executor;
}
I have autoReconnect=true&maxReconnects=10 on my db connection string.
It seems like the threads are being starved for a connection, but I don't understand why. There will always be more work items than there are threads. 150k records of work compared to 45 threads on the high end, and under 10k records of work on the low end. The application never threw these exceptions until multi threading was introduced. I have the connection pool max size (54) set higher than the number of threads I have (45).
Ive tried changing the number of threads, the max size of the connection pool, different size files and did tons of research. Please advise.

Java / JDBC connections aren't thread safe so each thread creates its own connections.
And, MySQL servers limit the number of simultaneous connections they allow. That's a hard limit set at MySQL server startup time. So it's possible your JDBC code in all your threads is attempting to make more connections than the server allows, and so the server rejects them. The app responds with the exceptions you saw.
org.springframework.dao.DataAccessResourceFailureException: Unable to acquire JDBC Connection;
There's another factor to keep in mind. Concurrent queries to the same table (INSERTs or anything else) can contend with one another. Paradoxically, you may get much better throughput with a much smaller number of threads. Try four threads.
If you give the command SHOW GLOBAL STATUS LIKE 'Connection%' you'll see a count of connection errors. Give the command before and after you run your program and take the difference between the values. The values look like this.
Connection_errors_accept errors that occurred during calls to accept() on the listening port.
Connection_errors_internal connections refused due to internal errors in the server, such as failure to start a new thread or an out-of-memory condition.
Connection_errors_max_connections connections refused because the server max_connections limit was reached.
Connection_errors_peer_address errors while searching for connecting client IP addresses.
Connection_errors_select errors during calls to OS select() or poll() on the listening port. (Failure of this operation does not necessarily means a client connection was rejected.)
Connection_errors_tcpwrap connections refused by the libwrap library.
Connections connection attempts (successful or not) to the MySQL server.

How do deal with h2 databases inability to deal with interrupts

How do deal with h2 database inability to deal with interrupts, I was occasionally seeing that my embedded h2 database appeared to get corrupted, in particular I had amended an ExecutorService so that if a task took too long it would cancel the task. The task would be cancelled okay but then subsequent database access failed with exceptions such as
23/07/2019 14.23.31:BST:DeleteDuplicatesController:start:SEVERE: commit failed
org.hibernate.TransactionException: commit failed
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:187)
at com.jthink.songkong.db.ReportCache.save(ReportCache.java:46)
at com.jthink.songkong.reports.AbstractReport.setReportDatabaseObject(AbstractReport.java:365)
at com.jthink.songkong.reports.DeleteDuplicatesReport.setReportDatabaseObject(DeleteDuplicatesReport.java:333)
at com.jthink.songkong.reports.DeleteDuplicatesReport.closeReport(DeleteDuplicatesReport.java:377)
at com.jthink.songkong.analyse.toplevelanalyzer.DeleteDuplicatesController.deleteAnyDups(DeleteDuplicatesController.java:606)
at com.jthink.songkong.analyse.toplevelanalyzer.DeleteDuplicatesController.start(DeleteDuplicatesController.java:665)
at com.jthink.songkong.ui.swingworker.DeleteDuplicates.doInBackground(DeleteDuplicates.java:43)
at com.jthink.songkong.ui.swingworker.DeleteDuplicates.doInBackground(DeleteDuplicates.java:20)
at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at javax.swing.SwingWorker.run(SwingWorker.java:334)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.hibernate.TransactionException: unable to commit against JDBC connection
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doCommit(JdbcTransaction.java:116)
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.commit(AbstractTransactionImpl.java:180)
... 14 more
Caused by: org.h2.jdbc.JdbcSQLNonTransientException: General error: "java.lang.IllegalStateException: Reading from nio:C:/Users/Paul/AppData/Roaming/SongKong/Database/Database.mv.db failed; file length -1 read length 4096 at 1541494 [1.4.199/1]"; SQL statement:
COMMIT [50000-199]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:502)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:427)
at org.h2.message.DbException.get(DbException.java:194)
at org.h2.message.DbException.convert(DbException.java:347)
at org.h2.command.Command.executeUpdate(Command.java:280)
at org.h2.jdbc.JdbcConnection.commit(JdbcConnection.java:542)
at com.mchange.v2.c3p0.impl.NewProxyConnection.commit(NewProxyConnection.java:1284)
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doCommit(JdbcTransaction.java:112)
... 15 more
Caused by: java.lang.IllegalStateException: Reading from nio:C:/Users/Paul/AppData/Roaming/SongKong/Database/Database.mv.db failed; file length -1 read length 4096 at 1541494 [1.4.199/1]
at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:883)
at org.h2.mvstore.DataUtils.readFully(DataUtils.java:420)
at org.h2.mvstore.FileStore.readFully(FileStore.java:98)
at org.h2.mvstore.MVStore.readBufferForPage(MVStore.java:1048)
at org.h2.mvstore.MVStore.readPage(MVStore.java:2186)
at org.h2.mvstore.MVMap.readPage(MVMap.java:554)
at org.h2.mvstore.Page$NonLeaf.getChildPage(Page.java:1086)
at org.h2.mvstore.Page.get(Page.java:221)
at org.h2.mvstore.MVMap.get(MVMap.java:402)
at org.h2.mvstore.MVMap.get(MVMap.java:389)
at org.h2.mvstore.MVStore.getMapName(MVStore.java:2737)
at org.h2.mvstore.MVStore.renameMap(MVStore.java:2650)
at org.h2.mvstore.tx.TransactionStore.commit(TransactionStore.java:453)
at org.h2.mvstore.tx.Transaction.commit(Transaction.java:389)
at org.h2.engine.Session.commit(Session.java:691)
at org.h2.command.dml.TransactionCommand.update(TransactionCommand.java:46)
at org.h2.command.CommandContainer.update(CommandContainer.java:133)
at org.h2.command.Command.executeUpdate(Command.java:267)
... 18 more
Caused by: java.nio.channels.ClosedChannelException
at sun.nio.ch.FileChannelImpl.ensureOpen(FileChannelImpl.java:110)
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:721)
at org.h2.store.fs.FileNio.read(FilePathNio.java:74)
at org.h2.mvstore.DataUtils.readFully(DataUtils.java:406)
... 34 more
23/07/2019 14.23.31:BST:Errors:addError:SEVERE: Adding Error:commit failed
I have since found this issue
Basically if using H2 in embedded mode, and it receives an interrupt then all subsequent access fails until the thread pool is close and reopened. In the example I give of a process having to be cancelled because it appears to be stuck there is no solution except for interrupting
I also have another case whereby usually the controller thread that doesn't directly do a database work itself so I was struggling to see why when an interrupt occurred why this would cause database errors since this is handled by controller thread. I have now worked out the issue is that Im using an ExecutorService with a fixed size BlockingQueue (so that we dont have a big queue build up in memory), but if the queue gets full then new task is actually executed by the controller thread (because of CallerRunsPolicy), so the controller thread can be making calls to database after all.
Im using H2 with hibernate and in both cases calling the following immediately after the interrupt
HibernateUtil.closeFactory();
seems to solve the issue, however I guess this means that any other threads with hibernate sessions will be broken, but at least newly opened sessins will be okay. So im not particularly happy with this workaround, any other ideas ?
Using H2 as a server is not a solution since the whole point of H2 was an embedded db self contained within application.

Although not properly documented using the async protocol allows a connection to be interrupted without breaking all other connections.

Hibernate "APPARENT DEADLOCK!!! Creating emergency threads for unassigned pending tasks!"

I recently got the following messages in our logs followed by a JVM crash (Due to OOME). I am not sure what to make of this and would really appreciate any guidance.
2015-03-19 21:15:02,457 [Timer-0] WARN (ThreadPoolAsynchronousRunner.java [run]:608) - com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#6824f21c -- APPARENT DEADLOCK!!! Creating emergency threads for unassigned pending tasks!
2015-03-19 21:26:29,543 [Timer-0] WARN (ThreadPoolAsynchronousRunner.java [run]:624) - com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#6824f21c -- APPARENT DEADLOCK!!! Complete Status:
Managed Threads: 3
Active Threads: 3
Active Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#15da1b6b (com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#2)
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#b35b08a (com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#1)
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#51cfdd17 (com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#0)
Pending Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#19397937
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#5c7d3838
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#7aea62dd
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#55622ff2
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#74004a8
Pool thread stack traces:
Thread[com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#0,5,main]
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:560)
Thread[com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#2,5,main]
java.net.SocketOutputStream.socketWrite0(Native Method)
java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:109)
java.net.SocketOutputStream.write(SocketOutputStream.java:153)
java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3227)
com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1917)
com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2060)
com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2536)
com.mysql.jdbc.ConnectionImpl.configureClientCharacterSet(ConnectionImpl.java:1751)
com.mysql.jdbc.ConnectionImpl.initializePropsFromServer(ConnectionImpl.java:3425)
com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2196)
com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:718)
com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
sun.reflect.GeneratedConstructorAccessor306.newInstance(Unknown Source)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:408)
com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:302)
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:135)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:182)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:171)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:137)
com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1014)
com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:32)
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1810)
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)
Thread[com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#1,5,main]
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:560)
2015-03-19 21:56:59,137 [Timer-0] WARN (ThreadPoolAsynchronousRunner.java [run]:608) - com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#6824f21c -- APPARENT DEADLOCK!!! Creating emergency threads for unassigned pending tasks!
2015-03-19 21:56:59,143 [eXistThread-18676] ERROR (XQueryServlet.java [process]:566) - Java heap space
java.lang.OutOfMemoryError: Java heap space
at org.exist.storage.btree.BTree$BTreeNode.read(BTree.java:1269)
at org.exist.storage.btree.BTree$BTreeNode.access$16(BTree.java:1239)
at org.exist.storage.btree.BTree.getBTreeNode(BTree.java:460)
at org.exist.storage.btree.BTree.scanSequential(BTree.java:413)
at org.exist.storage.btree.BTree$BTreeNode.scanNextPage(BTree.java:2039)
at org.exist.storage.btree.BTree$BTreeNode.query(BTree.java:1835)
at org.exist.storage.btree.BTree$BTreeNode.query(BTree.java:1759)
at org.exist.storage.btree.BTree$BTreeNode.query(BTree.java:1759)
at org.exist.storage.btree.BTree$BTreeNode.query(BTree.java:1759)
at org.exist.storage.btree.BTree$BTreeNode.access$12(BTree.java:1734)
at org.exist.storage.btree.BTree.query(BTree.java:379)
at org.exist.storage.structural.NativeStructuralIndexWorker.scanByType(NativeStructuralIndexWorker.java:259)
at org.exist.dom.VirtualNodeSet.getNodesFromIndex(VirtualNodeSet.java:457)
at org.exist.dom.VirtualNodeSet.realize(VirtualNodeSet.java:585)
at org.exist.dom.VirtualNodeSet.iterator(VirtualNodeSet.java:860)
at org.exist.dom.AbstractNodeSet.iterator(AbstractNodeSet.java:1)
at org.exist.storage.structural.NativeStructuralIndexWorker.findDescendantsByTagName(NativeStructuralIndexWorker.java:162)
at org.exist.xquery.LocationStep.getAttributes(LocationStep.java:645)
at org.exist.xquery.LocationStep.eval(LocationStep.java:434)
at org.exist.xquery.AbstractExpression.eval(AbstractExpression.java:71)
at org.exist.xquery.PathExpr.eval(PathExpr.java:264)
at org.exist.xquery.Predicate.selectByNodeSet(Predicate.java:446)
at org.exist.xquery.Predicate.evalPredicate(Predicate.java:326)
at org.exist.xquery.LocationStep.processPredicate(LocationStep.java:251)
at org.exist.xquery.LocationStep.applyPredicate(LocationStep.java:238)
at org.exist.xquery.LocationStep.eval(LocationStep.java:462)
at org.exist.xquery.AbstractExpression.eval(AbstractExpression.java:71)
at org.exist.xquery.PathExpr.eval(PathExpr.java:264)
at org.exist.xquery.LetExpr.eval(LetExpr.java:142)
at org.exist.xquery.LetExpr.eval(LetExpr.java:187)
at org.exist.xquery.LetExpr.eval(LetExpr.java:187)
at org.exist.xquery.BindingExpression.eval(BindingExpression.java:164)
2015-03-19 21:56:59,147 [Timer-0] WARN (ThreadPoolAsynchronousRunner.java [run]:624) - com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#6824f21c -- APPARENT DEADLOCK!!! Complete Status:
Managed Threads: 3
Active Threads: 3
Active Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#79180a12 (com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#0)
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#243c6d0c (com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#1)
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#50191373 (com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#2)
Pending Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#3a9d08ca
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#3ecdd11
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#44ff846d
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#5ce5850a
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#eec1d04
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#6b8d4d9d
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#53e9706d
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#23d472cf
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#4dbe4f8c
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#4c5e0203
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#54ac79fd
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask#546e2bad
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#6b13cc83
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#57e185f8
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#60357d68
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#45231180
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#3021aa73
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#6bb437ca
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#2021c9e9
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#7d53637c
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#409c2c97
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#adc5929
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#241ca71a
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#42b26866
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#636b1c33
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#b160466
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#4af34669
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#1b53e609
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#2062ebd4
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#1b6cfe8a
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#4b7c2380
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#4f9be748
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#78108924
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#474b002
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#2ebee32f
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#3e0fe017
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#42aa175b
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#637f5bac
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#3a017b77
com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#7b4f2b78
Pool thread stack traces:
Thread[com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#1,5,main]
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:408)
com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
com.mysql.jdbc.ResultSetImpl.getInstance(ResultSetImpl.java:370)
com.mysql.jdbc.MysqlIO.buildResultSetWithRows(MysqlIO.java:2532)
com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:477)
com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:2510)
com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:1746)
com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2135)
com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2536)
com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2465)
com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1383)
com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4826)
com.mysql.jdbc.IterateBlock.doForAll(IterateBlock.java:50)
com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4804)
com.mchange.v2.c3p0.impl.DefaultConnectionTester.activeCheckConnectionNoQuery(DefaultConnectionTester.java:185)
com.mchange.v2.c3p0.impl.DefaultConnectionTester.activeCheckConnection(DefaultConnectionTester.java:62)
com.mchange.v2.c3p0.AbstractConnectionTester.activeCheckConnection(AbstractConnectionTester.java:67)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.testPooledConnection(C3P0PooledConnectionPool.java:368)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.refurbishIdleResource(C3P0PooledConnectionPool.java:310)
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask.run(BasicResourcePool.java:1999)
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)
Thread[com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#2,5,main]
com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2596)
com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2465)
com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1383)
com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4826)
com.mysql.jdbc.IterateBlock.doForAll(IterateBlock.java:50)
com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4804)
com.mchange.v2.c3p0.impl.DefaultConnectionTester.activeCheckConnectionNoQuery(DefaultConnectionTester.java:185)
com.mchange.v2.c3p0.impl.DefaultConnectionTester.activeCheckConnection(DefaultConnectionTester.java:62)
com.mchange.v2.c3p0.AbstractConnectionTester.activeCheckConnection(AbstractConnectionTester.java:67)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.testPooledConnection(C3P0PooledConnectionPool.java:368)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.refurbishIdleResource(C3P0PooledConnectionPool.java:310)
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask.run(BasicResourcePool.java:1999)
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)
Thread[com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#0,5,main]
java.util.concurrent.ConcurrentHashMap.putVal(ConcurrentHashMap.java:1012)
java.util.concurrent.ConcurrentHashMap.put(ConcurrentHashMap.java:1006)
com.newrelic.agent.TransactionService.addTransaction(TransactionService.java:142)
com.newrelic.agent.Transaction.getTransaction(Transaction.java:1104)
com.newrelic.agent.Transaction.getTransaction(Transaction.java:1087)
com.newrelic.agent.TracerService$TracerServiceImpl.getTracer(TracerService.java:136)
com.newrelic.agent.TracerService.getTracer(TracerService.java:41)
com.newrelic.agent.instrumentation.InvocationPoint.invoke(InvocationPoint.java:55)
com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java)
com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4826)
com.mysql.jdbc.IterateBlock.doForAll(IterateBlock.java:50)
com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4804)
com.mchange.v2.c3p0.impl.DefaultConnectionTester.activeCheckConnectionNoQuery(DefaultConnectionTester.java:185)
com.mchange.v2.c3p0.impl.DefaultConnectionTester.activeCheckConnection(DefaultConnectionTester.java:62)
com.mchange.v2.c3p0.AbstractConnectionTester.activeCheckConnection(AbstractConnectionTester.java:67)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.testPooledConnection(C3P0PooledConnectionPool.java:368)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.refurbishIdleResource(C3P0PooledConnectionPool.java:310)
com.mchange.v2.resourcepool.BasicResourcePool$AsyncTestIdleResourceTask.run(BasicResourcePool.java:1999)
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)
We are using hiberanate and c3p0 with the following c3p0 configuration:
We are using the following maven artifacts for hibernate and c3p0:
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>4.3.6.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-c3p0</artifactId>
<version>4.3.6.Final</version>
</dependency>
with the following c3p0 configuration:
configuration = new Configuration().setProperty("hibernate.dialect", "org.hibernate.dialect.MySQL5InnoDBDialect")
.setProperty("hibernate.connection.provider_class", "org.hibernate.connection.C3P0ConnectionProvider")
.setProperty("hibernate.c3p0.idle_test_period", "1000")
.setProperty("hibernate.c3p0.min_size", "20")
.setProperty("hibernate.c3p0.max_size", "50")
.setProperty("hibernate.c3p0.timeout", "1800")
.setProperty("hibernate.c3p0.max_statements", "50")
The server is under very light load ~5 queries a second. (Java 8)

I stumbled into the same exception and the reason was a wrong password of the db user...
c3p0 you're a funny guy

So, directly the issue is that the Connection pool was trying to acquire new Connections, but the tasks attempting to acquire those tasks froze for a long period of time, so long that c3p0 decided the tasks must be deadlocked and then discarded and replaced the Thread pool. Later, the Thread pool was hung on idle connection test tasks.
Normally, "hung" tasks tend to look like the second Thread underneath the first "Pool thread stack traces:" label above: performing network IO that fails to complete. Your circumstances are odd in that two of the three threads are not stuck in IO. They have barely begun to do anything, yet they aren't live. Then you experience an OutOfMemoryError, and you get another APPARENT DEADLOCK on idle connection test tasks that also look like they mostly should be live.
Maybe your application is very close to some kind of resource limits that are causing things to run very sluggishly? Straightforwardly, you might increase the amount of memory available to this application (or modify it to have a lower memory footprint). You experience an OOME the second time the Thread pool tries to flush and recreate hung Threads, not directly provoked by that, but quite possibly caused by the growing Thread footprint. (In your logs, are there lots of these APPARENT DEADLOCKs previously? If you force a JVM Thread dump, do you see lots of com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread instances around, still hung on old, not completing tasks?
Some general comments: If your load is no more than 5-ish simultaneous queries, why such a heavy pool? why not min_size 5-ish, max 10-ish? Your max_statements setting is way too small for the number of Connections you permit in the pool. I'd omit this entirely until you get things working smoothly. Then, to get a bit better performance, you might set the more-straightforward-to-reason-about maxStatementsPerConnection parameter if you want.
Mostly you need to keep your application's footprint (memory? Threads?) well below the resources alotted to it, either by increasing resources, reducing its footprint, or fixing any issue that might exist that cause its resource footprint to increase into limits. I'd start by making the pool smaller, the available memory larger, and configuring the pool to be much smaller.

Authentication issue for me too. I just added the domain part to the database server name and it all worked. Very misleading error.

How to trace and prevent the deadlock appeared in c3po which is running in seperate processes?

I have a very simple computation which produces letter matrices finds probably all the words in the matrix. The letters in the word are adjacent cells.
for (int i = 0; i < 500; i++) {
System.out.println(i);
Matrix matrix = new Matrix(4);
matrix.scanWordsRandomly(9);
matrix.printMatrix();
System.out.println(matrix.getSollSize());
matrix.write_to_db();
}
Here is the persisting code.
public void write_to_db() {
Session session = null;
try {
session = HibernateUtil.getSessionFactory().openSession();
session.beginTransaction();
Matrixtr onematrixtr = new Matrixtr();
onematrixtr.setDimension(dimension);
onematrixtr.setMatrixstr(this.toString());
onematrixtr.setSolsize(getSollSize());
session.save(onematrixtr);
for (Map.Entry<Kelimetr, List<Cell>> sollution : sollutions.entrySet()) {
Kelimetr kelimetr = sollution.getKey();
List<Cell> solpath = sollution.getValue();
Solstr onesol = new Solstr();
onesol.setKelimetr(kelimetr);
onesol.setMatrixtr(onematrixtr);
onesol.setSoltext(solpath.toString().replace("[", "").replace("]", "").replace("true", "").replace("false", ""));
session.save(onesol);
}
session.getTransaction().commit();
session.close();
}
catch (HibernateException he) {
System.out.println("DB Error : " + he.getMessage());
session.close();
}
catch (Exception ex) {
System.out.println("General Error : " + ex.getMessage());
}
}
Here is the hibernate configuration file.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE hibernate-configuration PUBLIC "-//Hibernate/Hibernate Configuration DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-configuration-3.0.dtd">
<hibernate-configuration>
<session-factory>
<property name="hibernate.dialect">org.hibernate.dialect.MySQLDialect</property>
<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="hibernate.connection.url">jdbc:mysql://localhost:3306/kelimegame_db_dev?autoReconnect=true&useUnicode=true&characterEncoding=UTF-8</property>
<property name="hibernate.connection.username">root</property>
<property name="hibernate.connection.password">!.Wlu9RrCA</property>
<property name="hibernate.show_sql">false</property>
<property name="hibernate.query.factory_class">org.hibernate.hql.classic.ClassicQueryTranslatorFactory</property>
<property name="hibernate.format_sql">false</property>
<!-- Use the C3P0 connection pool provider -->
<property name="hibernate.c3p0.acquire_increment">50</property>
<property name="hibernate.c3p0.min_size">10</property>
<property name="hibernate.c3p0.max_size">100</property>
<property name="hibernate.c3p0.timeout">300</property>
<property name="hibernate.c3p0.max_statements">5</property>
<property name="hibernate.c3p0.idle_test_period">3000</property>
<mapping resource="kelimegame/entity/Progress.hbm.xml"/>
<mapping resource="kelimegame/entity/Solstr.hbm.xml"/>
<mapping resource="kelimegame/entity/Kelimetr.hbm.xml"/>
<mapping resource="kelimegame/entity/User.hbm.xml"/>
<mapping resource="kelimegame/entity/Achievement.hbm.xml"/>
<mapping resource="kelimegame/entity/Matrixtr.hbm.xml"/>
</session-factory>
</hibernate-configuration>
After finding all possible solutions I persist the matrix and the solutions using hibernate. I am also using c3pO library. I am not spawning any thread. All the work is being done in a very simple iterative way. But I am running the jar in separate processes.
From different terminals I am executing this :
java -jar NewDB.jar
I got a deadlock as follows :
Apr 25, 2013 8:38:05 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#7f0c09f9 -- APPARENT DEADLOCK!!! Creating emergency threads for unassigned pending tasks!
Apr 25, 2013 9:08:23 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#7f0c09f9 -- APPARENT DEADLOCK!!! Complete Status:
Managed Threads: 3
Active Threads: 3
Active Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#2933f261
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#1
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#116dd369
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#0
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#41529b6f
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#2
Pending Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#165ab5ea
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#1d5d211d
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#4d2905fa
Pool thread stack traces:
Thread[C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#1,5,main]
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:662)
Thread[C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#0,5,main]
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:662)
Thread[C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#2,5,main]
com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:662)
Apr 25, 2013 9:41:29 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#7f0c09f9 -- APPARENT DEADLOCK!!! Creating emergency threads for unassigned pending tasks!
Apr 25, 2013 9:55:18 PM com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector run
WARNING: com.mchange.v2.async.ThreadPoolAsynchronousRunner$DeadlockDetector#7f0c09f9 -- APPARENT DEADLOCK!!! Complete Status:
Managed Threads: 3
Active Threads: 3
Active Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#5a337b7d
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#0
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#69f079ce
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#1
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#2accf9b8
on thread: C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#2
Pending Tasks:
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#771eb4fb
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#fc07d6
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#2266731b
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#740f0341
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#59edbee
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#78e924
com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask#2123aba
com.mchange.v2.resourcepool.BasicResourcePool$ScatteredAcquireTask#7acd8a65
Pool thread stack traces:
Thread[C3P0PooledConnectionPoolManager[identityToken->z8kfsx8uibeyqevbbapc|4045cf35]-HelperThread-#0,5,main]
java.text.NumberFormat.getInstance(NumberFormat.java:769)
java.text.NumberFormat.getInstance(NumberFormat.java:393)
java.text.MessageFormat.subformat(MessageFormat.java:1262)
java.text.MessageFormat.format(MessageFormat.java:860)
java.text.Format.format(Format.java:157)
java.text.MessageFormat.format(MessageFormat.java:836)
com.mysql.jdbc.Messages.getString(Messages.java:106)
com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:2552)
com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3002)
com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2991)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3532)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:943)
com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:4113)
com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1308)
com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2336)
com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2176)
com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2158)
com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:792)
com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
sun.reflect.GeneratedConstructorAccessor7.newInstance(Unknown Source)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:525)
com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:381)
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:305)
com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:134)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:183)
com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:172)
com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:188)Killed
caglar#ubuntu:~/NetBeansProjects/NewDB/dist$
My question is as follows :
Can this deadlock in c3po happen since I am running the program in
separate processes?
Should I use one process and multiple threads inside of this
process?
How can I trace this deadlock understand the cause of it? Is there a way to trace multiple JVMs causing deadlocks?

this is an interesting one.
you've published two distinct APPARENT DEADLOCKS. the first one is being caused by c3p0 attempting to close() Connections, and those close() operations are neither succeeding nor failing with an Exception in a timely manner. the second APPARENT DEADLOCK shows problems with Connection acquisition: c3p0 is attempting to acquire new Connections, and those attempts are neither succeeding nor failing with an Exception in a timely manner. the fact that very different operations are freezing suggests that it might be a more general problem with your dbms locking up under the stress of what you are doing or somesuch. it should be no problem to run multiple processes against your database, but you need to stay cognizant of limits.
there are a few interesting things about your configuration:
1) hibernate.c3p0.max_statements=5 is a very bad idea, on almost any pool and particularly on pools this large. you've got up to 100 Connections, and you're only allowing a total of 5 Statements to be cached between all of them. this might stress both the pool and the DBMS, as you will constantly be churning through PreparedStatements and the statement cache does a lot of bookkeeping about that. you may have meant that to be 5 cached statements per connection, but that's not what you have configured. you have set a global maximum for your pool. maybe try hibernate.c3p0.maxStatementsPerConnection=5 instead? or set max_statements to zero to turn statement caching off, at least until you resolve your deadlock. see http://www.mchange.com/projects/c3p0/#configuring_statement_pooling
2) if you are running your computation in multiple processes rather than multiple Threads, do you really need each process to hold 50 - 100 Connections? things may well be freezing up simply because you are stressing the dbms with too many Connections outstanding as each of your multiple processes acquire lots of resource-heavy Connections. you don't need more Connections in any process than you might have client Threads running concurrently within that process. i'd set hibernate.c3p0.acquire_increment and probably hibernate.c3p0.max_size to much smaller values.
3) if you really do need all those Connections running simultaneously, you can reduce the vulnerability of your pools to deadlock by increasing the config parameter numHelperThreads to some value greater than its default of 3. you probably want numHelperThreads to be something like twice the number of cores available on your machine. given that you are running multiple processes though, you might find that you are saturating your CPU, and that is freezing things up. so watch for that.
basically, try updating your configuration so that you are using resources -- file handles, network connections, CPU -- as efficiently as possible and so that you are not unnecessarily stressing the pool / statement cache / dbms more than you need to be.
if these suggestions don't resolve the problem, please post the fill config of your pools. c3p0 dumps its config at INFO level on pool initialization.
good luck!

c3p0 hangs in awaitAvailable with hibernate

I have console application that hangs during execution. Here is my configuration:
cfg.setProperty("hibernate.connection.driver_class", "com.mysql.jdbc.Driver");
cfg.setProperty("hibernate.connection.url", "jdbc:mysql://localhost:3306/db?user=db&password=db");
cfg.setProperty("hibernate.connection.username", "db");
cfg.setProperty("hibernate.connection.password", "db");
cfg.setProperty("hibernate.connection.pool_size", "5");
cfg.setProperty("hibernate.connection.autocommit", "false");
cfg.setProperty("hibernate.c3p0.min_size", "5");
cfg.setProperty("hibernate.c3p0.max_size", "20");
cfg.setProperty("hibernate.c3p0.timeout", "300");
cfg.setProperty("hibernate.c3p0.max_statements", "50");
cfg.setProperty("hibernate.c3p0.idle_test_period", "3000");
Here is my stacktrace:
"main" prio=10 tid=0x000000000168f800 nid=0x1c37 in Object.wait() [0x00007fa60d0ad000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
- waiting on <0x00000007400f4c68> (a com.mchange.v2.resourcepool.BasicResourcePool)
at com.mchange.v2.resourcepool.BasicResourcePool.awaitAvailable(BasicResourcePool.java:1315)
at com.mchange.v2.resourcepool.BasicResourcePool.prelimCheckoutResource(BasicResourcePool.java:557)
- locked <0x00000007400f4c68> (a com.mchange.v2.resourcepool.BasicResourcePool)
at com.mchange.v2.resourcepool.BasicResourcePool.checkoutResource(BasicResourcePool.java:477)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool.checkoutPooledConnection(C3P0PooledConnectionPool.java:525)
at com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource.getConnection(AbstractPoolBackedDataSource.java:128)
at org.hibernate.service.jdbc.connections.internal.C3P0ConnectionProvider.getConnection(C3P0ConnectionProvider.java:84)
at org.hibernate.internal.AbstractSessionImpl$NonContextualJdbcConnectionAccess.obtainConnection(AbstractSessionImpl.java:281)
at org.hibernate.engine.jdbc.internal.LogicalConnectionImpl.obtainConnection(LogicalConnectionImpl.java:297)
at org.hibernate.engine.jdbc.internal.LogicalConnectionImpl.getConnection(LogicalConnectionImpl.java:169)
at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doBegin(JdbcTransaction.java:67)
at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.begin(AbstractTransactionImpl.java:160)
at org.hibernate.internal.SessionImpl.beginTransaction(SessionImpl.java:1392)
at org.kriyak.parser.IndexArchiveRapid.indexFile(IndexArchiveRapid.java:70)
at org.kriyak.parser.IndexArchiveRapid.main(IndexArchiveRapid.java:53)
I open only one conencton and it doesn't seem that I leak them. And also I use one thread. I haven't adjusted any mysql settings except memory usage. Mysql works fine from console. Why can this happen? Is this c3p0 error?

does this happen immediately, or after a while? that is, do checkouts initially succeed, but then hang like this? if so, it looks like a Connection leak. please try setting c3p0 params unreturnedConnectionTimeout and debugUnreturnedConnectionStackTraces to see if there is a leak. See
http://www.mchange.com/projects/c3p0/#configuring_to_debug_and_workaround_broken_clients , http://www.mchange.com/projects/c3p0/#unreturnedConnectionTimeout , http://www.mchange.com/projects/c3p0/#debugUnreturnedConnectionStackTraces .
if this happens immediately, if no Connections are successfully checked out, the question is whether the pool ever succeeds at acquiring Connections. by default, if it never does succeed, after about 30 seconds your thread should break with a failure. (it doesn't look like you've done this, but if for example you'd set acquireRetryAttempts to zero, c3p0 might hang indefinitely waiting for Connections.)
to debug c3p0 issues, it's helpful to capture the version and config information that c3p0 dumps to logs at INFO level on pool initialization.
good luck!

Also, you haven't seem to initialize the checkoutTime parameter for c3p0, which specifies the amount of time a client should wait for acquiring a connection from the connection pool.
see http://www.mchange.com/projects/c3p0/#checkoutTimeout

You may need to increase c3p0.numHelperThreads. The helper threads are responsible for creating new database connections and adding them to the pool. If there aren't enough threads to keep up with demand then application threads will be stuck waiting in awaitAvailable(). To confirm this is the case look at all the HelperThreads and see if they are all in use and in the process of connecting to the database.