無法關閉Tomcat內的Neo4j Jetty服務器webapp

目前我正在開發一個使用Neo4j的web應用程序。我們的應用程序需要部署在Tomcat環境中（客戶需求）。我們決定嵌入Neo4j，因爲這樣我們可以使用Neo4j提供的Java API，它更易於部署，並且性能得到改善。但是，我們還需要訪問REST API，因爲我們有一個使用Angular編寫的單頁web應用程序，目前正在使用此接口。但是，嵌入式Neo4j數據庫不公開REST API。 Neo4j服務器工件包含可以使用嵌入式圖形數據庫引導碼頭服務器的代碼。所以我們的Tomcat webapp啓動了一個Jetty服務器。我們可以通過在一個端口（8080）上部署Tomcat的webapp以及在另一個端口（7474）上的Neo4j REST接口和Neo4j瀏覽器來訪問graphDb。雖然這有點奇怪，但它工作正常，除了當我們試圖阻止我們的Web應用程序（例如重新部署）。當關閉我們的web應用程序，我們收到這些錯誤從Tomcat：無法關閉Tomcat內的Neo4j Jetty服務器webapp

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 [[email protected]{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 [[email protected]{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 [[email protected]]) and a value of type [org.eclipse.jetty.http.HttpFields.DateGenerator] (value [[email protected]]) 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$$anon$1] (value [[email protected]]) and a value of type [java.lang.Integer] (value [0]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks 
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [[email protected]]) 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$$anon$1] (value [[email protected]]) and a value of type [java.lang.Integer] (value [0]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks 
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [[email protected]]) 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$$anon$1] (value [[email protected]]) and a value of type [java.lang.Integer] (value [0]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks 
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [[email protected]]) 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$$anon$1] (value [[email protected]]) and a value of type [java.lang.Integer] (value [0]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks 
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [[email protected]]) 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$$anon$1] (value [[email protected]]) and a value of type [java.lang.Integer] (value [0]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks 
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [[email protected]]) 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$$anon$1] (value [[email protected]]) and a value of type [java.lang.Integer] (value [0]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks 
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [[email protected]]) 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$$anon$1] (value [[email protected]]) and a value of type [java.lang.Integer] (value [0]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks 
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [[email protected]]) 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$$anon$1] (value [[email protected]]) and a value of type [java.lang.Integer] (value [0]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
jun 10, 2014 6:43:17 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks 
SEVERE: The web application [/chainmonitor] created a ThreadLocal with key of type [scala.util.DynamicVariable$$anon$1] (value [[email protected]]) 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 [[email protected]]) 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

我們的pom.xml如下：

<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>

這是我們如何啓動嵌入式數據庫並啓動碼頭服務器：

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

當前neo4j-server.properties爲空。我沒有嘗試過很多不同的配置，但是這樣做似乎不成問題。

這是我們如何停止嵌入式數據庫和碼頭服務器：

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

這顯然是Tomcat的內存泄漏防護（http://wiki.apache.org/tomcat/MemoryLeakProtection）引起的。

結果是我們的webapp只能通過完全殺死Tomcat進程（kill -9）來重新部署，這是非常不可取的。

我們已經嘗試了一堆東西：

沒有關閉嵌入式grapbDb。沒有效果。
未明確關閉引導程序。沒有效果。（引導程序有自己的關閉鉤子）
先關閉引導程序，然後關閉嵌入式數據庫。
線程免責：https://github.com/Neo4j/Neo4j/issues/1070。代碼運行並移除了59個線程本地值，但沒有明顯效果。有趣的是，當我在停機期間循環運行一分鐘時，它一直說它將6個值固定。對我來說，這表明這個過程根本不起作用，因爲Neo4j在關機時需要一些時間。
關機後延遲。我們嘗試這樣做的原因是因爲在tomcat收到關閉信號後，我們需要等待幾秒鐘才能真正殺死進程，否則我們在下一次啓動時出現錯誤，表明我們的圖形數據已損壞（消息沒有被正確關閉）。延遲5秒以上似乎也有影響，因爲之後我們只得到6次嚴重錯誤而不是16次。這也是爲什麼我認爲焚燒過程根本不起作用的原因。
我們嘗試將我們的嵌入式Neo4j添加到集羣，因此可以同時使用REST API和嵌入式Neo4j。然而，經過大約四個小時試圖讓這個工作，我們放棄了。在嵌入式Neo4j數據庫的啓動過程中，我們的web應用程序剛剛凍結。經過一些調試後，它非常像Neo4j代碼中的死鎖。我們嘗試將所有HA超時配置設置爲一些較小的值，但不起作用。

該問題是由Neo4j碼頭服務器引起的。沒有它，這個問題不會出現。儘管我們需要REST API。你知道我們如何解決這個問題嗎？或者您有沒有其他方法可以在Tomcat環境中使用嵌入式數據庫和REST API？

我們使用：

的Java：1.7.0_60
的Tomcat 7.0.54
的Neo4j：2.0.3（我們已經嘗試2.1.1，但得到完全相同的結果）
在Windows 7和Linux上觀察到相同的問題Redhat

來源

2014-06-12 Lodewijk Bogaards

如果您「需要」Neo4j REST API，那麼您應該運行Neo4j服務器。請注意，Neo4j服務器支持非託管擴展，它們是Java代碼並且可以完全訪問Java API。 Neo4j服務器負責通過與REST API使用的相同的HTTP服務器提供對這些API的訪問。 –

您可能泄漏的交易尚未關閉，那麼Neo4j會等待20秒關閉關閉這些交易。

如果您等待5秒以上，那些報告的問題仍然存在？

來源

2014-06-15 19:50:39

即使我剛啓動Neo4j並關閉它，我也會遇到這個問題。我也等了120秒，沒有明顯的效果。 –

我們有一個非常類似的設置和需要。這是我們解決這個問題的解決方案。 JVM Runtime shutdownHook在Tomcat中不起作用，因此我們持有對包含GraphDatabaseService的包裝器對象的引用，並將該包裝器放入存儲器管理器對象中。對資源庫管理器對象中的方法使用@PreDestroy批註，這會在資源庫管理器類被銷燬之前關閉資源庫。

import javax.annotation.PreDestroy;

...

@PreDestroy 
public void destroy() { 
    log.info("Destroying Neo4jRepositoryManager..."); 
    shutdown(Neo4jPropertyKeys.SANDBOX_DATABASE.getUrlKey()); 
    shutdown(Neo4jPropertyKeys.PRODUCTION_DATABASE.getUrlKey()); 
    shutdown(Neo4jPropertyKeys.TEST_DATABASE.getUrlKey()); 
} 

private void shutdown(String urlKey) { 
    if(repositories.containsKey(urlKey)) { 
     LabeledNodeGraphRepository graphdb = repositories.get(urlKey); 
     graphdb.getGraphDatabaseService().shutdown(); 
     log.info(urlKey + " shutdown..."); 
    } 
} 

<bean id="repositoryManager" class="mypath.neo4j.repository.Neo4jRepositoryManager"/>

我們的環境是：

的Java 1.7.0_72
的Tomcat 7.0.56
Neo4j的2.1.6
春4.0 .5
Jersey 2.1.4

來源

2015-01-30 00:36:25 danbsd

無法關閉Tomcat內的Neo4j Jetty服務器webapp

回答

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