无法关闭Tomcat webapp中的Neo4j Jetty服务器

Question

目前，我正在开发一个利用Neo4J的webapp。我们的应用程序需要部署在Tomcat环境中（客户需求）。我们决定嵌入Neo4j，因为这样我们可以使用Neo4j提供的Java API，部署起来更容易，性能也更好。但是，我们还需要访问REST API，因为我们有一个用Angular编写的单页webapp，目前正在使用这个接口。但是，嵌入式Neo4j数据库并不公开REST API。Neo4j-server工件包含可以用嵌入式图形数据库引导jetty服务器的代码。因此，我们的Tomcat webapp正在启动一个Jetty服务器。我们可以通过部署在一个端口（8080）上的Tomcat中的webapp，以及另一个端口（7474）上的Neo4j REST接口和Neo4j浏览器来访问graphDb。尽管这有点奇怪，但它工作得很好，除非我们试图停止我们的webapp（例如重新部署）。当关闭webapp时，我们从Tomcat收到以下错误：

SEVERE: The web application [/chainmonitor] appears to have started a thread named [GC-Monitor] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [RRD4J Sync Pool [Thread-1]] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [Statistics Gatherer[primitives]] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [pool-1-thread-1] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [pool-1-thread-2] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [DateCache] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [qtp835579386-31-selector-3] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [qtp835579386-32-selector-0] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [qtp835579386-33-selector-1] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [qtp835579386-34-selector-2] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [qtp835579386-35-selector-4] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [qtp835579386-36-selector-5] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [qtp835579386-37-acceptor-0-ServerConnector@1425c689{HTTP/1.1}{localhost:7474}] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [qtp835579386-38-acceptor-1-ServerConnector@1425c689{HTTP/1.1}{localhost:7474}] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [HashSessionScavenger-0] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/chainmonitor] appears to have started a thread named [qtp835579386-54] but has failed to stop it. This is very likely to create a memory leak.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [org.eclipse.jetty.http.HttpFields$1] (value [org.eclipse.jetty.http.HttpFields$1@4a3d3a5e]) and a value of type [org.eclipse.jetty.http.HttpFields.DateGenerator] (value [org.eclipse.jetty.http.HttpFields$DateGenerator@24f0137b]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [scala.util.DynamicVariable$$anon$1@281a099d]) and a value of type [java.lang.Integer] (value [0]) 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.
jun 10, 2014 6:43:27 PM org.apache.catalina.startup.HostConfig undeploy
INFO: Undeploying context [/chainmonitor]
jun 10, 2014 6:43:27 PM org.apache.catalina.startup.ExpandWar deleteDir
SEVERE: [C:\dev\apache-tomcat-7.0.54\webapps\chainmonitor\WEB-INF\lib] could not be completely deleted. The presence of the remaining files may cause problems
jun 10, 2014 6:43:27 PM org.apache.catalina.startup.ExpandWar deleteDir
SEVERE: [C:\dev\apache-tomcat-7.0.54\webapps\chainmonitor\WEB-INF] could not be completely deleted. The presence of the remaining files may cause problems
jun 10, 2014 6:43:27 PM org.apache.catalina.startup.ExpandWar deleteDir
SEVERE: [C:\dev\apache-tomcat-7.0.54\webapps\chainmonitor] could not be completely deleted. The presence of the remaining files may cause problems
jun 10, 2014 6:43:27 PM org.apache.catalina.startup.ExpandWar delete
SEVERE: [C:\dev\apache-tomcat-7.0.54\webapps\chainmonitor] could not be completely deleted. The presence of the remaining files may cause problems

我们的pom.xml如下所示：

    <dependency>
        <groupId>org.neo4j</groupId>
        <artifactId>neo4j</artifactId>
        <version>2.0.3</version>
    </dependency>
    <dependency>
        <groupId>org.neo4j.app</groupId>
        <artifactId>neo4j-server</artifactId>
        <version>2.0.3</version>
    </dependency>

这就是我们如何启动嵌入式数据库和jetty服务器：

graphDb = (EmbeddedGraphDatabase) new GraphDatabaseFactory().
      newEmbeddedDatabaseBuilder(dataDir).loadPropertiesFromURL(Neo4jPropertiesUrl).newGraphDatabase();
bootstrapper = new WrappingNeoServerBootstrapper(graphDb);

当前neo4j-server.properties为空。我没有尝试过很多不同的配置，但这样做似乎不是问题。

这就是我们停止嵌入式数据库和jetty服务器的方法：

    @Override
    public void contextDestroyed(ServletContextEvent event) {
​            graphDb.shutdown();
            bootstrapper.stop();
    }

这显然是由Tomcat的内存泄漏保护（http://wiki.apache.org/tomcat/memoryleakprotection）造成的。

结果是，我们的webapp只能通过完全杀死Tomcat进程(kill-9)来重新部署，这是非常不可取的。

我们试过很多方法：

• 未关闭嵌入的GrapbDB。没有影响。
• 未显式关闭引导程序。没有效果。（引导程序有自己的关机钩子）
• 先关闭引导程序，然后关闭嵌入式数据库。
• 线程点燃器:https://github.com/neo4j/neo4j/issues/1070。代码运行并牺牲了59个线程本地值，但没有明显的效果。有趣的是，当我在关机期间循环运行一分钟时，它一直说它牺牲了6个值。对我来说，这表明这个过程根本不起作用，因为Neo4j在关闭时需要一些时间。
• 关机后延迟。我们尝试这样做的原因是，在tomcat收到一个关闭信号后，我们需要等待几秒钟才能真正关闭进程，否则在下一次启动时会出现一个错误，即我们的图数据已经损坏（带有一个没有正确关闭的消息）。延迟5+秒似乎也有影响，因为之后我们只得到6个严重错误，而不是16个。这也是我认为自焚过程根本不起作用的原因。
• 我们尝试将嵌入式Neo4j添加到集群中，这样就可以使用RESTAPI作为wel和嵌入式Neo4j。然而，在大约四个小时试图让这个工作后，我们放弃了。在启动嵌入式Neo4j数据库期间，我们的webapplication只是冻结了。经过一些调试之后，它在Neo4J的代码中看起来像是一个死锁。我们试图将所有HA超时配置设置为一些较小的值，但没有效果。

这个问题是由Neo 4 J jetty服务器引起的。没有它，这个问题就不会出现。不过我们需要REST API。你知道我们怎么解决这个问题吗？或者您是否有其他方法在Tomcat环境中使用嵌入式数据库和REST API？

我们正在使用：

• java:1.7.0_60
• Tomcat 7.0.54
• neo4j:2.0.3（我们尝试了2.1.1，但得到了完全相同的结果）
• 在Windows7和Linux Redhat上也发现了同样的behviour

Answer 1

您可能有尚未关闭的泄漏事务，然后Neo4j在关闭时等待长达20秒来关闭这些事务。

如果您等待5秒以上，报告的问题中还有哪些？