Mybatis, BoneCP, Spring: SQLBuilder Memory leak issue in Tomcat 7.0.* [closed] - spring

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Closed 10 years ago.
I'm working on a project using Spring, Mybatis and BoneCP.
Every time I stop Tomcat server, I observe the following mem leak issues:
Dec 23, 2012 5:20:21 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/project] appears to have started a thread named [com.google.common.base.internal.Finalizer] but has failed to stop it. This is very likely to create a memory leak.
Dec 23, 2012 5:20:21 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/project] appears to have started a thread named [Memcached IO over {MemcachedConnection to /127.0.0.1:11211}] but has failed to stop it. This is very likely to create a memory leak.
Dec 23, 2012 5:20:21 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/project] appears to have started a thread named [transcoder-1-1] but has failed to stop it. This is very likely to create a memory leak.
Dec 23, 2012 5:20:21 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/project] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal#386602aa]) and a value of type [org.apache.ibatis.jdbc.SqlBuilder.SQL] (value [org.apache.ibatis.jdbc.SqlBuilder$SQL#313903d3]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Dec 23, 2012 5:20:21 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/project] created a ThreadLocal with key of type [jsr166y.ThreadLocalRandom$1] (value [jsr166y.ThreadLocalRandom$1#162a2ae4]) and a value of type [jsr166y.ThreadLocalRandom] (value [jsr166y.ThreadLocalRandom#2a65ea1a]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
The number of SqlBuilder seems increase for every database access. Your help/comment is very appreciated.
Here are my configurations:
pom.xml
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.firefly</groupId>
<artifactId>ArcaneAeon</artifactId>
<name>project</name>
<packaging>war</packaging>
<version>1.0.0-BUILD-SNAPSHOT</version>
<properties>
<java-version>1.6</java-version>
<org.springframework-version>3.1.0.RELEASE</org.springframework-version>
<org.aspectj-version>1.6.9</org.aspectj-version>
<org.slf4j-version>1.6.6</org.slf4j-version>
</properties>
<dependencies>
<dependency>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.4.3</version>
</dependency>
<!-- MyBatis -->
<dependency>
<groupId>org.mybatis</groupId>
<artifactId>mybatis</artifactId>
<version>3.1.1</version>
</dependency>
<!-- <dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>5.1.21</version>
</dependency> -->
<dependency>
<groupId>cglib</groupId>
<artifactId>cglib</artifactId>
<version>2.2.2</version>
</dependency>
<!-- Connection Pooling -->
<dependency>
<groupId>com.jolbox</groupId>
<artifactId>bonecp-spring</artifactId>
<version>0.7.1.RELEASE</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>13.0.1</version>
</dependency>
<dependency>
<groupId>org.mybatis</groupId>
<artifactId>mybatis-spring</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>org.mybatis.caches</groupId>
<artifactId>mybatis-memcached</artifactId>
<version>1.0.0-beta1</version>
</dependency>
<!-- Redis -->
<dependency>
<groupId>redis.clients</groupId>
<artifactId>jedis</artifactId>
<version>2.1.0</version>
</dependency>
<!-- Spring -->
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-core-asl</artifactId>
<version>1.9.9</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>1.9.9</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<version>${org.springframework-version}</version>
<exclusions>
<!-- Exclude Commons Logging in favor of SLF4j -->
<exclusion>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
<version>${org.springframework-version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>${org.springframework-version}</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>${org.springframework-version}</version>
</dependency>
<!-- Spring Security -->
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-core</artifactId>
<version>3.1.2.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-config</artifactId>
<version>3.1.2.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-aspects</artifactId>
<version>3.1.2.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-cas</artifactId>
<version>3.1.2.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-crypto</artifactId>
<version>3.1.2.RELEASE</version>
</dependency>
<dependency>
<groupId>org.springframework.security</groupId>
<artifactId>spring-security-web</artifactId>
<version>3.1.2.RELEASE</version>
</dependency>
<!-- AspectJ -->
<dependency>
<groupId>org.aspectj</groupId>
<artifactId>aspectjrt</artifactId>
<version>${org.aspectj-version}</version>
</dependency>
<!-- Logging -->
<dependency>
<groupId>javax.mail</groupId>
<artifactId>mail</artifactId>
<version>1.4.5</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${org.slf4j-version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${org.slf4j-version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>${org.slf4j-version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>apache-log4j-extras</artifactId>
<version>1.1</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
<exclusions>
<exclusion>
<groupId>javax.mail</groupId>
<artifactId>mail</artifactId>
</exclusion>
<exclusion>
<groupId>javax.jms</groupId>
<artifactId>jms</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.jdmk</groupId>
<artifactId>jmxtools</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.jmx</groupId>
<artifactId>jmxri</artifactId>
</exclusion>
</exclusions>
<scope>runtime</scope>
</dependency>
<!-- #Inject -->
<dependency>
<groupId>javax.inject</groupId>
<artifactId>javax.inject</artifactId>
<version>1</version>
</dependency>
<!-- Servlet -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
<scope>provided</scope>
</dependency>
<!-- <dependency>
<groupId>javax.servlet.jsp</groupId>
<artifactId>jsp-api</artifactId>
<version>2.1</version>
<scope>provided</scope>
</dependency> -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>jstl</artifactId>
<version>1.2</version>
</dependency>
<!-- Test -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.10</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<version>3.1.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.mybatis.generator</groupId>
<artifactId>mybatis-generator-core</artifactId>
<version>1.3.2</version>
</dependency>
<dependency>
<groupId>org.springframework.data</groupId>
<artifactId>spring-data-redis</artifactId>
<version>1.0.2.RELEASE</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.12.2</version>
<configuration>
<argLine>-Denvironment="development"</argLine>
</configuration>
</plugin>
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.7</version>
<executions>
<execution>
<id>default-cli</id>
<phase>deploy</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<tasks>
<echo message="Copying war package to server....."/>
<scp
file="....."
todir="....."
password="....." trust="true" />
<echo message="Complete copying war package to server....."/>
<echo message="Executing deploy script on server...."/>
<sshexec
username="....."
password="....."
host="....."
trust="true"
command="......"/>
<echo message="Finish deploying...."/>
</tasks>
</configuration>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant-jsch</artifactId>
<version>1.8.4</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.9</version>
<configuration>
<additionalProjectnatures>
<projectnature>org.springframework.ide.eclipse.core.springnature</projectnature>
</additionalProjectnatures>
<additionalBuildcommands>
<buildcommand>org.springframework.ide.eclipse.core.springbuilder</buildcommand>
</additionalBuildcommands>
<downloadSources>true</downloadSources>
<downloadJavadocs>true</downloadJavadocs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
<compilerArgument>-Xlint:all</compilerArgument>
<showWarnings>true</showWarnings>
<showDeprecation>true</showDeprecation>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.2.1</version>
<configuration>
<mainClass>org.test.int1.Main</mainClass>
</configuration>
</plugin>
</plugins>
</build>
</project>
root-context.xml
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:p="http://www.springframework.org/schema/p"
xmlns:context="http://www.springframework.org/schema/context"
xmlns:security="http://www.springframework.org/schema/security"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="
http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context.xsd
http://www.springframework.org/schema/security http://www.springframework.org/schema/security/spring-security.xsd">
<!-- Root Context: defines shared resources visible to all other web components -->
<context:annotation-config />
<context:component-scan base-package="com.firefly.lcgame" />
<!-- Load Properties Files -->
<context:property-placeholder location="classpath*:*-${environment}.properties"/>
<!-- Spring Data Redis -->
<bean id="connectionFactory"
class="org.springframework.data.redis.connection.jedis.JedisConnectionFactory">
<property name="hostName" value="${redis.host}" />
<property name="port" value="${redis.port}" />
<property name="password" value="${redis.pass}" />
<property name="usePool" value="${redis.pooling}" />
<property name="poolConfig" ref="jedisPoolConfig" />
</bean>
<bean id="jedisPoolConfig" class="redis.clients.jedis.JedisPoolConfig">
<property name="maxActive" value="${redis.maxActive}" />
<property name="minIdle" value="${redis.minIdle}" />
<property name="testOnBorrow" value="${redis.testOnBorrow}" />
</bean>
<bean id="redisTemplate" class="org.springframework.data.redis.core.RedisTemplate"
p:connection-factory-ref="connectionFactory" />
<!-- BoneCP configuration -->
<bean id="dataSource" class="com.jolbox.bonecp.BoneCPDataSource" destroy-method="close">
<property name="driverClass" value="${jdbc.driverClassName}" />
<property name="jdbcUrl" value="${jdbc.url}" />
<property name="username" value="${jdbc.username}"/>
<property name="password" value="${jdbc.password}"/>
<property name="idleConnectionTestPeriodInMinutes" value="${boneCP.idleConnectionTestPeriodInMinutes}"/>
<property name="idleMaxAgeInMinutes" value="${boneCP.idleMaxAgeInMinutes}"/>
<property name="maxConnectionsPerPartition" value="${boneCP.maxConnectionsPerPartition}"/>
<property name="minConnectionsPerPartition" value="${boneCP.minConnectionsPerPartition}"/>
<property name="partitionCount" value="${boneCP.partitionCount}"/>
<property name="acquireIncrement" value="${boneCP.acquireIncrement}"/>
<property name="statementsCacheSize" value="${boneCP.statementsCacheSize}"/>
<property name="releaseHelperThreads" value="${boneCP.releaseHelperThreads}"/>
<property name="lazyInit" value="true"/>
<property name="maxConnectionAgeInSeconds" value="${boneCP.maxConnectionAgeInSeconds}"/>
</bean>
<bean id="sqlSessionFactory" class="org.mybatis.spring.SqlSessionFactoryBean">
<property name="dataSource" ref="dataSource" />
<!-- <property name="configLocation" value="classpath:mybatis-config.xml" /> -->
</bean>
<bean id="transactionManager"
class="org.springframework.jdbc.datasource.DataSourceTransactionManager">
<property name="dataSource" ref="dataSource" />
</bean>
<bean id="mappers" class="org.mybatis.spring.mapper.MapperScannerConfigurer">
<property name="basePackage" value="com.firefly.lcgame.dao" />
<!-- <property name="sqlSessionFactoryBeanName" value="sqlSessionFactory" /> -->
</bean>
<bean class="org.springframework.web.servlet.mvc.annotation.DefaultAnnotationHandlerMapping"/>
<bean
class="org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter">
<property name="messageConverters">
<list>
<ref bean="jsonConverter" />
<!-- <ref bean="marshallingConverter" />
<ref bean="atomConverter" /> -->
</list>
</property>
</bean>
<bean id="jsonConverter"
class="org.springframework.http.converter.json.MappingJacksonHttpMessageConverter">
<property name="supportedMediaTypes" value="application/json" />
</bean>
<bean id="localeResolver" class="org.springframework.web.servlet.i18n.AcceptHeaderLocaleResolver"/>
<!-- localization -->
<bean id="messageSource" class="org.springframework.context.support.ReloadableResourceBundleMessageSource"
p:fallbackToSystemLocale="false" p:useCodeAsDefaultMessage="true" p:defaultEncoding="UTF-8">
<description>Base message source to handle internationalization</description>
<property name="basenames">
<list>
<value>classpath:localization/messages</value>
</list>
</property>
</bean>
<bean id="annotationMethodHandlerExceptionResolver" class="org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerExceptionResolver">
<property name="order" value="0"/>
</bean>
<bean id="restExceptionResolver" class="com.firefly.lcgame.exceptions.handler.RestExceptionHandler">
<property name="order" value="100"></property>
<property name="errorResolver">
<bean class="com.firefly.lcgame.exceptions.handler.DefaultRestErrorResolver">
<property name="localeResolver" ref="localeResolver"></property>
<!-- <property name="defaultMoreInfoUrl" value="mailto:support#mycompany.com"></property> -->
<property name="exceptionMappingDefinitions">
<map>
<!-- 404 -->
<entry key="com.firefly.lcgame.exceptions.InvalidAccessExeption" value="404, 1, error.invalid.access, _exmsg"></entry>
<!-- 500 (catch all): -->
<entry key="Throwable" value="500, 1, error.internal, _exmsg"></entry>
</map>
</property>
</bean>
</property>
</bean>
<!-- Secure Rest Service Configuration -->
<!-- <security:http create-session="never" entry-point-ref="digestEntryPoint">
<security:intercept-url pattern="/duty/stages**" access="ROLE_USER, ROLE_ADMIN" />
<security:http-basic />
<security:custom-filter ref="digestFilter" after="BASIC_AUTH_FILTER" />
</security:http> -->
<security:http pattern="/login**" security="none">
</security:http>
<security:http pattern="/dummy**">
<security:intercept-url pattern="/dummy**" access="ROLE_USER, ROLE_ADMIN"/>
<security:http-basic/>
</security:http>
<security:http pattern="/**" entry-point-ref="digestEntryPoint" >
<security:intercept-url pattern="/**" access="ROLE_USER, ROLE_ADMIN"/>
<security:custom-filter ref="digestFilter" position="BASIC_AUTH_FILTER"/>
</security:http>
<bean id="digestFilter" class="org.springframework.security.web.authentication.www.DigestAuthenticationFilter">
<property name="userDetailsService" ref="userService" />
<property name="authenticationEntryPoint" ref="digestEntryPoint" />
</bean>
<bean id="digestEntryPoint" class="org.springframework.security.web.authentication.www.DigestAuthenticationEntryPoint">
<property name="realmName" value="Arcane Aeon Digest Secure REST-WS"/>
<property name="key" value="0606e6c2-cee4-3259-9d3e-27d484d716b0"/>
<property name="nonceValiditySeconds" value="10"/>
</bean>
<security:authentication-manager>
<security:authentication-provider user-service-ref="userService"/>
</security:authentication-manager>
<bean id="userService" class="com.firefly.lcgame.services.CustomerUserDetailsService">
</bean>
</beans>
web.xml
<?xml version="1.0" encoding="UTF-8"?>
<web-app xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://java.sun.com/xml/ns/javaee" xmlns:web="http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd" version="2.5">
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>/WEB-INF/spring/root-context.xml</param-value>
</context-param>
<listener>
<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
</listener>
<!-- Secure Rest Service Configuration -->
<filter>
<filter-name>springSecurityFilterChain</filter-name>
<filter-class>org.springframework.web.filter.DelegatingFilterProxy</filter-class>
</filter>
<filter-mapping>
<filter-name>springSecurityFilterChain</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<servlet>
<servlet-name>appServlet</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value>/WEB-INF/spring/appServlet/servlet-context.xml</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>appServlet</servlet-name>
<url-pattern>/</url-pattern>
</servlet-mapping>
</web-app>