Develop Reference

SQLite in-memory database encounters SQLITE_LOCKED_SHAREDCACHE intermittently

I am using mybatis 3.4.6 along with org.xerial:sqlite-jdbc 3.28.0. Below is my configuration to use an in-memory database with shared mode enabled
db.driver=org.sqlite.JDBC
db.url=jdbc:sqlite:file::memory:?cache=shared
The db.url is correct according to this test class
And I managed to setup the correct transaction isolation level with below mybatis configuration though there is a typo of property read_uncommitted according to this issue which is reported by me as well
<environment id="${db.env}">
<transactionManager type="jdbc"/>
<dataSource type="POOLED">
<property name="driver" value="${db.driver}" />
<property name="url" value="${db.url}"/>
<property name="username" value="${db.username}" />
<property name="password" value="${db.password}" />
<property name="defaultTransactionIsolationLevel" value="1" />
<property name="driver.synchronous" value="OFF" />
<property name="driver.transaction_mode" value="IMMEDIATE"/>
<property name="driver.foreign_keys" value="ON"/>
</dataSource>
</environment>
This line of configuration
<property name="defaultTransactionIsolationLevel" value="1" />
does the trick to set the correct value of PRAGMA read_uncommitted
I am pretty sure of it since I debugged the underneath code which initialize the connection and check the value has been set correctly
However with the above setting, my program still encounters SQLITE_LOCKED_SHAREDCACHE intermittently while reading, which I think it shouldn't happen according the description highlighted in the red rectangle of below screenshot. I want to know the reason and how to resolve it, though the occurring probability of this error is low.
Any ideas would be appreciated!!
The debug configurations is below
===CONFINGURATION==============================================
jdbcDriver org.sqlite.JDBC
jdbcUrl jdbc:sqlite:file::memory:?cache=shared
jdbcUsername
jdbcPassword ************
poolMaxActiveConnections 10
poolMaxIdleConnections 5
poolMaxCheckoutTime 20000
poolTimeToWait 20000
poolPingEnabled false
poolPingQuery NO PING QUERY SET
poolPingConnectionsNotUsedFor 0
---STATUS-----------------------------------------------------
activeConnections 5
idleConnections 5
requestCount 27
averageRequestTime 7941
averageCheckoutTime 4437
claimedOverdue 0
averageOverdueCheckoutTime 0
hadToWait 0
averageWaitTime 0
badConnectionCount 0
===============================================================
Attachments:
The exception is below
org.apache.ibatis.exceptions.PersistenceException:
### Error querying database. Cause: org.apache.ibatis.transaction.TransactionException: Error configuring AutoCommit. Your driver may not support getAutoCommit() or setAutoCommit(). Requested setting: false. Cause: org.sqlite.SQLiteException: [SQLITE_LOCKED_SHAREDCACHE] Contention with a different database connection that shares the cache (database table is locked)
### The error may exist in mapper/MsgRecordDO-sqlmap-mappering.xml
### The error may involve com.super.mock.platform.agent.dal.daointerface.MsgRecordDAO.getRecord
### The error occurred while executing a query
### Cause: org.apache.ibatis.transaction.TransactionException: Error configuring AutoCommit. Your driver may not support getAutoCommit() or setAutoCommit(). Requested setting: false. Cause: org.sqlite.SQLiteException: [SQLITE_LOCKED_SHAREDCACHE] Contention with a different database connection that shares the cache (database table is locked)

I finally resolved this issue by myself and share the workaround below in case someone else encounters similar issue in the future.
First of all, we're able to get the completed call stack of the exception shown below
Going through the source code indicated by the callback, we have below findings.
SQLite is built-in with auto commit enabled by default which is contradict with MyBatis which disables auto commit by default since we're using SqlSessionManager
MyBatis would override the auto commit property during connection initialization using method setDesiredAutoCommit which finally invokes SQLiteConnection#setAutoCommit
SQLiteConnection#setAutoCommit would incur a begin immediate operation against the database which is actually exclusive, check out below source code screenshots for detailed explanation since we configure our transaction mode to be IMMEDIATE
<property name="driver.transaction_mode" value="IMMEDIATE"/>
So until now, An apparent solution is to change the transaction mode to be DEFERRED. Furthermore, the solution of making the auto commit setting the same between MyBatis and SQLite has been considered as well, however, it's not adopted since there is no way to set the auto commit of SQLiteConnection during initialization stage, there would be always switching (from true to false or vice versa) and switch would cause the above error probably if transaction mode is not set properly

SpringMVC, c3p0, hibernate, JPA Application leaking Connections leads to Too Many Connections error

I've googled and searched stackoverflow for a solution to my problem for over 4 hours now, reading and trying to learn what is happening but I have not come across a solution that pertains to my issue so apologies if this sounds like a duplicate, I'll try my best to explain exactly what is happening so I can get some insight into the inner workings of c3p0.
I have a SpringMVC web application running on Tomcat with Hibernate, JPA, and C3P0 as my pooling resource. On page reload, the application as it stand makes a few calls to the database to get a random image and display it on the new page. The application runs fine for about 30 or so page reloads but always eventually crashes and I have to restart mysql in order for the application to work again, it gives the following error:
Apr 04, 2015 12:21:55 PM com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask run
WARNING: com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#634d8e3d -- Acquisition Attempt Failed!!! Clearing pending acquires. While trying to acquire a needed new resource, we failed to succeed more than the maximum number of allowed acquisition attempts (30). Last acquisition attempt exception:
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Data source rejected establishment of connection, message from server: "Too many connections"
at sun.reflect.GeneratedConstructorAccessor101.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.Util.getInstance(Util.java:386)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:989)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:975)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1114)
at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2493)
at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2526)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2311)
at com.mysql.jdbc.ConnectionImpl.(ConnectionImpl.java:834)
at com.mysql.jdbc.JDBC4Connection.(JDBC4Connection.java:47)
at sun.reflect.GeneratedConstructorAccessor43.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:347)
at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:135)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:182)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:171)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:137)
at com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1014)
at com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:32)
at com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1810)
at com.mchange.v2.async.ThreadPerTaskAsynchronousRunner$TaskThread.run(ThreadPerTaskAsynchronousRunner.java:255)
Here are pertaining files/configurations to give context to the problem:
spring.xml:
<context:component-scan base-package="com.clathrop.infographyl.dao" />
<bean id="entityManagerFactory"
class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean">
<property name="persistenceUnitName" value="infographylPU" />
<property name="dataSource" ref="dataSource" />
</bean>
<bean id="dataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource" destroy-method="close">
<!-- Connection properties -->
<property name="driverClass" value="com.mysql.jdbc.Driver" />
<property name="jdbcUrl" value="jdbc:mysql://localhost:3306/infographyl_db" />
<property name="user" value="user" />
<property name="password" value="passwd" />
<!-- Pool properties -->
<property name="minPoolSize" value="5" />
<property name="maxPoolSize" value="20" />
<property name="acquireIncrement" value="1" />
<property name="maxStatements" value="0" />
<property name="idleConnectionTestPeriod" value="3000" />
<property name="loginTimeout" value="300" />
</bean>
<bean id="transactionManager" class="org.springframework.orm.jpa.JpaTransactionManager">
<property name="entityManagerFactory" ref="entityManagerFactory" />
</bean>
persistence.xml:
<persistence-unit name="infographylPU" transaction-type="RESOURCE_LOCAL">
<class>com.clathrop.infographyl.model.Infographic</class>
<provider>org.hibernate.ejb.HibernatePersistence</provider>
<properties>
<property name="hibernate.dialect" value="org.hibernate.dialect.MySQL5Dialect"/>
</properties>
</persistence-unit>
Here is what a basic query looks like, in this class I have an EntityManager as an instance variable and i close() the entityManager after every query is finished but it has no affect on the number of connections made in the database.
InfographicDaoImpl.java:
#Repository
public class InfographicDaoImpl implements InfographicDao{
#PersistenceContext
private EntityManager entityManager;
#Override
#Transactional
public void insertInfographic(Infographic infographic){
try{
entityManager.persist(infographic);
} catch (Exception e){
e.printStackTrace();
} finally {
entityManager.close();
}
}
#Override
public List<Infographic> findAllInfographics(){
try{
CriteriaBuilder builder = entityManager.getCriteriaBuilder();
CriteriaQuery<Infographic> cq = builder.createQuery(Infographic.class);
Root<Infographic> root = cq.from(Infographic.class);
cq.select(root);
List<Infographic> igList = entityManager.createQuery(cq).getResultList();
return igList;
} catch (Exception e){
e.printStackTrace();
return null;
} finally {
entityManager.close();
}
}
#Override
public Infographic getRandomInfographic(Integer tableSize){
Random rand = new Random();
int randomIndex = rand.nextInt((tableSize-1)+1) + 1;
try{
CriteriaBuilder builder = entityManager.getCriteriaBuilder();
CriteriaQuery<Infographic> cq = builder.createQuery(Infographic.class);
Root<Infographic> root = cq.from(Infographic.class);
cq.select(root);
cq.where(builder.equal(root.<Integer>get("id"), randomIndex));
Infographic randomIg = entityManager.createQuery(cq).getSingleResult();
return randomIg;
} catch (Exception e){
e.printStackTrace();
return null;
} finally {
entityManager.close();
}
}
#Override
public Integer getRowCount(){
try{
Number result = (Number) entityManager.createNativeQuery("Select count(id) from infographics").getSingleResult();
return result.intValue();
} catch (Exception e){
e.printStackTrace();
return null;
} finally {
entityManager.close();
}
}
#Override
public List<Infographic> listInfographics(Integer startIndex, Integer pageSize){
List<Infographic> igList = new ArrayList<Infographic>();
String sStartIndex = Integer.toString(startIndex);
String sPageSize = Integer.toString(pageSize);
try{
List list = entityManager.createNativeQuery("Select * from infographics limit " + sStartIndex + ", " + sPageSize).getResultList();
for(Object ig : list){
igList.add((Infographic) ig);
}
return igList;
} catch(Exception e){
e.printStackTrace();
return null;
} finally {
entityManager.close();
}
}
}
At this point I have a few questions as to what is happening in my application. The way I understand it is that c3p0 is handling connections made to the database and I thought that with a pooled connection, the connections made would be reused but instead I am getting a growing list of more connections when I look at the processlist in mysql. The number of connections keeps growing until the application finally throws the too many connection warning shown above. My question is why is c3p0 not reusing the connections? Am I missing a configuration somewhere to tell it to reuse the pre-existing connections? Why does entityManager.close() seemingly have no affect? If I am misunderstanding how to use hibernate and c3p0 please let me know what I am missing. Any help is greatly appreciate, thanks in advance.
UPDATE:
SEVERE: The web application [/infographyl] appears to have started a thread named [com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#0] but has failed to stop it. This is very likely to create a memory leak.
I've narrowed down the problem to a memory leak that is being recognized when tomcat starts up and deploys the application in question. My issue now is trying to find what possible configuration (or missing config) is causing the issue.
My current workaround is to set the wait_timeout in my.cnf to kill processes/connections that are older than 5 seconds, this seems to be ok for now but it is not a sustainable solution and I'd like to know the correct way to close my connections.
UPDATE2:
com.mchange.* INFO log:
Apr 05, 2015 10:57:30 PM org.hibernate.service.jdbc.connections.internal.ConnectionProviderInitiator instantiateExplicitConnectionProvider
INFO: HHH000130: Instantiating explicit connection provider: org.hibernate.ejb.connection.InjectedDataSourceConnectionProvider
Apr 05, 2015 10:57:30 PM com.mchange.v2.c3p0.impl.AbstractPoolBackedDataSource getPoolManager
INFO: Initializing c3p0 pool... com.mchange.v2.c3p0.ComboPooledDataSource [ acquireIncrement -> 1, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, dataSourceName -> z8kfsx98137ghpr10fde73|6aa74262, debugUnreturnedConnectionStackTraces -> false, description -> null, driverClass -> com.mysql.jdbc.Driver, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> z8kfsx98137ghpr10fde73|6aa74262, idleConnectionTestPeriod -> 3000, initialPoolSize -> 3, jdbcUrl -> jdbc:mysql://localhost:3306/infographyl_db, lastAcquisitionFailureDefaultUser -> null, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 0, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 20, maxStatements -> 0, maxStatementsPerConnection -> 0, minPoolSize -> 5, numHelperThreads -> 3, numThreadsAwaitingCheckoutDefaultUser -> 0, preferredTestQuery -> null, properties -> {user=******, password=******}, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> false, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false ]

So, from everything that you've described, it sounds like your application is creating and then abandoning multiple c3p0 pools. You don't experience what would be the usual symptom of exhaustion of a single pool (application freezes). Instead, your app opens more Connections than maxPoolSize, and then fails when it hits server-side Connection limits. Unless your server things ~20 Connections is too many, you are likely to be creating more than one pool. Setting wait_timeout hides the problem, as the Connections of the abandonned DataSources get automatically close()ed, but it won't be a good solution. If you are making new DataSources for each client, you'll dramatically slow down rather than speed up your app, and if those DataSources are not close()ed (it seems they aren't, or you'd not accumulate open Connections), you'll create Thread and memory leaks.
So.
First, how are you logging things? Please make sure that com.mchange.* classes are logged at INFO, and check look for pool initiation messages. c3p0 dumps a large pool config message at INFO on DataSource initialization. Make sure you see at least one of those messages. Do you see them many times? Then that is the problem.
If I am right and you are opening then abandoning multiple c3p0 DataSources, the next question becomes why. Pooled DataSources in your app are embedded in an EntityManagerFactory object, of which there should be just one for the lifetime of your application. Spring makes things look easy, but it hides the details of how/when things are constructed, destroyed, etc. I think the key question you may have to answer is why/whether Spring is creating multiple EntityManagerFactory instances (or recreating the c3p0 DataSource multiple times within a single EntityManagerFactory).
p.s. c3p0 offers no "loginTimeout" config parameter.

I've found a solution to my problem but I'm not quite sure it is the best approach.
I set wait_timeout in my.cnf to 5 seconds via:
[mysqld]
wait_timeout=5
This seems to be effective in destroying the sleeping processes that entityManager is creating and allowing me to run the app for extended periods of time without having to restart mysql.
My question now is, is this really the best and only way to deal with connections that are created by c3p0 + EntityManager? Why doesn't c3p0 destroy the connections or remove them on its own? Is this intended? Any clarification or discussion is appreciated. Thanks all :)

I think, that some of DB operations are causing exceptions. In such case Exception is thrown and the EntityManager is not closed as it should. Normally your db operations should looks like
EntityManager em=getEntityManagerSomehow();
try{
do your stuff with db here
}catch(Exception ex){
handle exception here eg. log or rethrow.
}finally{
em.close(); // always close entity manager even if exception occures.
}
In my opinion, if you refactor your code like shown abowe, problem will be fixed.

JDBC Maximum connection

i am stuck on this problem for the past 2 days, i have a webservice that extract Data from a local database converts it to XML sends to another webservice with HttpGet and gets the response of success or faile and updates my local database. After some time i start to get this Error:
java.sql.SQLException: Couldn't get connection because we are at maximum connection count (20/20) and there are none available
I have tried increasing the maxconnection in my server.xml and applicationContext but nothing changes, always after some time this happens,
This is my datasource
<!-- Data sources -->
<bean id="dataSourceStore" name="dataSourceStore" class="org.springframework.jndi.JndiObjectFactoryBean" destroy-method="close">
<property name="jndiName">
<value>java:comp/env/jdbc/StoreDS</value>
</property>
<property name="removeAbandoned" value="true"/>
<property name="initialSize" value="250" />
<property name="maxActive" value="350" />
</bean>
I have 2 methods that queries de Database, after them i use this one to close
public void close() {
try {
if (!this.getJdbcTemplate().getDataSource().getConnection().isClosed()) {
this.getJdbcTemplate().getDataSource().getConnection().close();
}
} catch (Exception e) {
e.printStackTrace();
// Logger.getLogger(myDAOImpl.class.getName()).log(Level.SEVERE, null, e);
}
}
Heres one example
public void updateStatus(Integer id, String name) {
super.getJdbcTemplate().update(
QueryUtil.QueryAtualizaPedido,
name, id);
close();
}
My server.xml also has maxActive="250", i tried to change this several times but the error always comes as 20/20
The server encountered an internal error () that prevented it from fulfilling this request.</u></p><p><b>exception</b> <pre>org.hibernate.exception.GenericJDBCException: Cannot open connection org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:126) org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:114) org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66) org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:52) org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:449) org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167) org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedConnectionProxy.java:74) com.sun.proxy.$Proxy221.prepareStatement(Unknown Source) br.com.fiorde.dao.conexao.connect.PreparedSt(connect.java:54) br.com.fiorde.servlets.webservice.ImportPedidoXML.validaUsuario(ImportPedidoXML.java:137) br.com.fiorde.servlets.webservice.ImportPedidoXML.doPost(ImportPedidoXML.java:93) br.com.fiorde.servlets.webservice.ImportPedidoXML.doGet(ImportPedidoXML.java:80)javax.servlet.http.HttpServlet.service(HttpServlet.java:617) javax.servlet.http.HttpServlet.service(HttpServlet.java:717) org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)</pre></p><p><b>root cause</b> <pre>java.sql.SQLException: Couldn't get connection because we are at maximum connection count (20/20) and there are none available org.logicalcobwebs.proxool.Prototyper.quickRefuse(Prototyper.java:309) org.logicalcobwebs.proxool.ConnectionPool.getConnection(ConnectionPool.java:152) org.logicalcobwebs.proxool.ProxoolDriver.connect(ProxoolDriver.java:89) java.sql.DriverManager.getConnection(DriverManager.java:571) java.sql.DriverManager.getConnection(DriverManager.java:233) org.hibernate.connection.ProxoolConnectionProvider.getConnection(ProxoolConnectionProvider.java:75) org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:446) org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167) org.hibernate.jdbc.BorrowedConnectionProxy.invoke(BorrowedConnectionProxy.java:74) com.sun.proxy.$Proxy221.prepareStatement(Unknown Source) br.com.fiorde.dao.conexao.connect.PreparedSt(connect.java:54) br.com.fiorde.servlets.webservice.ImportPedidoXML.validaUsuario(ImportPedidoXML.java:137) br.com.fiorde.servlets.webservice.ImportPedidoXML.doPost(ImportPedidoXML.java:93) br.com.fiorde.servlets.webservice.ImportPedidoXML.doGet(ImportPedidoXML.java:80) javax.servlet.http.HttpServlet.service(HttpServlet.java:617) javax.servlet.http.HttpServlet.service(HttpServlet.java:717) org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)

This usually is a result of failing to close connections when you are done using them. This is known as a connection leak.
Are you closing connections when you are done using them?

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!

PostgreSQL + Hibernate + C3P0 = FATAL: sorry, too many clients already

I have the following code
Configuration config = new Configuration().configure();
config.buildMappings();
serviceRegistry = new ServiceRegistryBuilder().applySettings(config.getProperties()).buildServiceRegistry();
SessionFactory factory = config.buildSessionFactory(serviceRegistry);
Session hibernateSession = factory.openSession();
Transaction tx = hibernateSession.beginTransaction();
ObjectType ot = (ObjectType)hibernateSession.merge(someObj);
tx.commit();
return ot;
hibernate.cfg.xml contains:
<session-factory>
<property name="connection.url">jdbc:postgresql://127.0.0.1:5432/dbase</property>
<property name="hibernate.dialect">org.hibernate.dialect.PostgreSQLDialect</property>
<property name="connection.driver_class">org.postgresql.Driver</property>
<property name="connection.username">username</property>
<property name="connection.password">password</property>
<property name="connection.provider_class">org.hibernate.connection.C3P0ConnectionProvider</property>
<property name="hibernate.c3p0.acquire_increment">1</property>
<property name="hibernate.c3p0.min_size">5</property>
<property name="hibernate.c3p0.max_size">20</property>
<property name="hibernate.c3p0.max_statements">50</property>
<property name="hibernate.c3p0.timeout">300</property>
<property name="hibernate.c3p0.idle_test_period">3000</property>
<property name="hibernate.c3p0.acquireRetryAttempts">1</property>
<property name="hibernate.c3p0.acquireRetryDelay">250</property>
<property name="hibernate.show_sql">true</property>
<property name="hibernate.use_sql_comments">true</property>
<property name="hibernate.transaction.factory_class">org.hibernate.transaction.JDBCTransactionFactory</property>
<property name="hibernate.current_session_context_class">thread</property>
<mapping class="...." />
</session-factory>
After a few seconds and some successful inserts, the following exception appears:
org.postgresql.util.PSQLException: FATAL: sorry, too many clients already
at org.postgresql.core.v3.ConnectionFactoryImpl.doAuthentication(ConnectionFactoryImpl.java:291)
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:108)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
at org.postgresql.jdbc2.AbstractJdbc2Connection.<init>(AbstractJdbc2Connection.java:125)
at org.postgresql.jdbc3.AbstractJdbc3Connection.<init>(AbstractJdbc3Connection.java:30)
at org.postgresql.jdbc3g.AbstractJdbc3gConnection.<init>(AbstractJdbc3gConnection.java:22)
at org.postgresql.jdbc4.AbstractJdbc4Connection.<init>(AbstractJdbc4Connection.java:30)
at org.postgresql.jdbc4.Jdbc4Connection.<init>(Jdbc4Connection.java:24)
at org.postgresql.Driver.makeConnection(Driver.java:393)
at org.postgresql.Driver.connect(Driver.java:267)
at com.mchange.v2.c3p0.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:135)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:182)
at com.mchange.v2.c3p0.WrapperConnectionPoolDataSource.getPooledConnection(WrapperConnectionPoolDataSource.java:171)
at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.acquireResource(C3P0PooledConnectionPool.java:137)
at com.mchange.v2.resourcepool.BasicResourcePool.doAcquire(BasicResourcePool.java:1014)
at com.mchange.v2.resourcepool.BasicResourcePool.access$800(BasicResourcePool.java:32)
at com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask.run(BasicResourcePool.java:1810)
at com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)
12:24:19.151 [ Thread-160] WARN internal.JdbcServicesImpl - HHH000342: Could not obtain connection to query metadata : Connections could not be acquired from the underlying database!
12:24:19.151 [ Thread-160] INFO dialect.Dialect - HHH000400: Using dialect: org.hibernate.dialect.PostgreSQLDialect
12:24:19.151 [ Thread-160] INFO internal.LobCreatorBuilder - HHH000422: Disabling contextual LOB creation as connection was null
12:24:19.151 [ Thread-160] INFO internal.TransactionFactoryInitiator - HHH000268: Transaction strategy: org.hibernate.engine.transaction.internal.jdbc.JdbcTransactionFactory
12:24:19.151 [ Thread-160] INFO ast.ASTQueryTranslatorFactory - HHH000397: Using ASTQueryTranslatorFactory
12:24:19.151 [ Thread-160] INFO hbm2ddl.SchemaUpdate - HHH000228: Running hbm2ddl schema update
12:24:19.151 [ Thread-160] INFO hbm2ddl.SchemaUpdate - HHH000102: Fetching database metadata
12:24:19.211 [Runner$PoolThread-#0] WARN resourcepool.BasicResourcePool - com.mchange.v2.resourcepool.BasicResourcePool$AcquireTask#ee4084 -- Acquisition Attempt Failed!!! Clearing pending acquires. While trying to acquire a needed new resource, we failed to succeed more than the maximum number of allowed acquisition attempts (1). Last acquisition attempt exception:
org.postgresql.util.PSQLException: FATAL: sorry, too many clients already
at org.postgresql.core.v3.ConnectionFactoryImpl.doAuthentication(ConnectionFactoryImpl.java:291)
It seems that the hibernate doesn't realse the connection. But hibernateSession.close() causes exception Session is closed because tx.commit() is called.

I'm not quite sure what's going on here, but I'd recommend you not set hibernate.c3p0.acquireRetryAttempts to 1. First, that renders your next setting, hibernate.c3p0.acquireRetryDelay irrelevant -- that sets the length of time between retry attempts, but if there is only one attempt (ok, the param name is misleading, it sets the total number of tries), there are no retries. The effect of your settings is simply to have the pool try to fetch a Connection whenever a client comes in, then throw an Exception to clients immediately if that fails. It doesn't at all limit the number of Connections the pool will try to acquire (unless you set breakOnAcquireFailure to true, in which case, with your settings, any failure to acquire a Connection would invalidate the whole pool).
I share sola's concern about your lack of reliable resource cleanup. If, under your settings, commit() means close() (and you are not allowed to call close explicitly? that seems bad), then it is commit that should be in the finally block (but commit in a finally block also seems bad, sometimes you don't want to commit). Whatever the issue with close/commit, with the code you have, occasional Exceptions between openSession and commit will lead to Connection leaks.
But that should not be the cause of your too-many-open-Connections problem. If you leak Connections, you'll find that the Connection pool eventually freezes (as maxPoolSize Connectiosn are checked out forever due to the leaks). You'd only have 25 open Connections. Something else is going on. Try reviewing your logs. Is more than one Connection pool somehow being initialized? (c3p0 dumps config information at INFO level on pool init, so if multiple pools are getting opened, you should see multiple messages. alternatively, you can inspect running c3p0 pools via JMX, to see whether/why more than 25 Connections have been opened.)
Good luck!

I found the cause why c3p0 behaved in this way.The issue was quite trivial...
This part of code:
Configuration config = new Configuration().configure();
config.buildMappings();
serviceRegistry = new ServiceRegistryBuilder().applySettings(config.getProperties()).buildServiceRegistry();
SessionFactory factory = config.buildSessionFactory(serviceRegistry);
was executed multiple times. Thank you Steve for the tip.

I'm suggesting you to use try-catch-finally block,
in finally kindly close the session
i.e
try {
tx.commit();
} catch (HibernateException e) {
handleException(e);
} finally {
hibernateSession.close();
}
and also,
the max_connections property in postgresql.conf it's 100 by default. Increase it if you need.