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Posted to users@jena.apache.org by Sorin Gheorghiu <so...@uni-konstanz.de> on 2018/11/30 14:13:30 UTC
Fuseki as a Web application in Docker
Hi,
the first attempt to start fuseki as a web application within a Docker
with Apache, Tomcat and Elasticsearch images succeded.
But after a restart (i.e. docker-compose down/up) it failed with
'Illegal access' error. Moreover a reboot didn't help, the error still
occurs.
Do you have any idea wheater is this related to fuseki or not? As well
any clue how to fix it?
Thank you in advance
30-Nov-2018 14:49:58.857 INFO [main]
org.apache.catalina.core.StandardEngine.startInternal Starting Servlet
Engine: Apache Tomcat/8.5.35
30-Nov-2018 14:49:59.289 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployWAR Deploying web
application archive [/usr/local/tomcat/webapps/fuseki.war]
30-Nov-2018 14:50:31.033 INFO [localhost-startStop-1]
org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was
scanned for TLDs yet contained no TLDs. Enable debug logging for this
logger for a complete list of JARs that were scanned but no TLDs were
found in them. Skipping unneeded JARs during scanning can improve
startup time and JSP compilation time.
30-Nov-2018 14:50:55.757 SEVERE [localhost-startStop-1]
org.apache.catalina.core.StandardContext.startInternal One or more
listeners failed to start. Full details will be found in the appropriate
container log file
30-Nov-2018 14:50:55.860 SEVERE [localhost-startStop-1]
org.apache.catalina.core.StandardContext.startInternal Context [/fuseki]
startup failed due to previous errors
30-Nov-2018 14:50:56.063 WARNING [localhost-startStop-1]
org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads
The web application [fuseki] appears to have started a thread named
[elasticsearch[_client_][[timer]]] but has failed to stop it. This is
very likely to create a memory leak. Stack trace of thread:
java.lang.Thread.sleep(Native Method)
org.elasticsearch.threadpool.ThreadPool$EstimatedTimeThread.run(ThreadPool.java:498)
30-Nov-2018 14:50:56.080 WARNING [localhost-startStop-1]
org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads
The web application [fuseki] appears to have started a thread named
[elasticsearch[_client_][scheduler][T#1]] but has failed to stop it.
This is very likely to create a memory leak. Stack trace of thread:
sun.misc.Unsafe.park(Native Method)
java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)
java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
java.lang.Thread.run(Thread.java:748)
30-Nov-2018 14:50:56.104 WARNING [localhost-startStop-1]
org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads
The web application [fuseki] appears to have started a thread named
[elasticsearch[_client_][transport_client_boss][T#1]] but has failed to
stop it. This is very likely to create a memory leak. Stack trace of thread:
sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:93)
sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:746)
io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:391)
io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:858)
java.lang.Thread.run(Thread.java:748)
30-Nov-2018 14:50:56.106 SEVERE [localhost-startStop-1]
org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks
The web application [fuseki] created a ThreadLocal with key of type
[java.lang.ThreadLocal] (value [java.lang.ThreadLocal@1ec7c10]) and a
value of type [io.netty.util.internal.InternalThreadLocalMap] (value
[io.netty.util.internal.InternalThreadLocalMap@45226f45]) but failed to
remove it when the web application was stopped. Threads are going to be
renewed over time to try and avoid a probable memory leak.
30-Nov-2018 14:50:56.120 SEVERE [localhost-startStop-1]
org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks
The web application [fuseki] created a ThreadLocal with key of type
[java.lang.ThreadLocal] (value [java.lang.ThreadLocal@1ec7c10]) and a
value of type [io.netty.util.internal.InternalThreadLocalMap] (value
[io.netty.util.internal.InternalThreadLocalMap@1593114a]) but failed to
remove it when the web application was stopped. Threads are going to be
renewed over time to try and avoid a probable memory leak.
30-Nov-2018 14:50:56.248 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployWAR Deployment of web
application archive [/usr/local/tomcat/webapps/fuseki.war] has finished
in [56,952] ms
30-Nov-2018 14:50:56.268 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
application directory [/usr/local/tomcat/webapps/examples]
30-Nov-2018 14:50:58.528 INFO [elasticsearch[_client_][scheduler][T#1]]
org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading
Illegal access: this web application instance has been stopped already.
Could not load
[org.elasticsearch.common.util.concurrent.ThreadContext$ContextPreservingAbstractRunnable].
The following stack trace is thrown for debugging purposes as well as to
attempt to terminate the thread which caused the illegal access.
java.lang.IllegalStateException: Illegal access: this web application
instance has been stopped already. Could not load
[org.elasticsearch.common.util.concurrent.ThreadContext$ContextPreservingAbstractRunnable].
The following stack trace is thrown for debugging purposes as well as to
attempt to terminate the thread which caused the illegal access.
at
org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading(WebappClassLoaderBase.java:1348)
at
org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1336)
at
org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1195)
at
org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1156)
at
org.elasticsearch.common.util.concurrent.ThreadContext.preserveContext(ThreadContext.java:273)
at
org.elasticsearch.common.util.concurrent.EsThreadPoolExecutor.wrapRunnable(EsThreadPoolExecutor.java:159)
at
org.elasticsearch.common.util.concurrent.EsThreadPoolExecutor.execute(EsThreadPoolExecutor.java:89)
at
org.elasticsearch.threadpool.ThreadPool$ThreadedRunnable.run(ThreadPool.java:455)
at
org.elasticsearch.threadpool.ThreadPool$LoggingRunnable.run(ThreadPool.java:419)
at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at
java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at
java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
30-Nov-2018 14:50:59.071 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
application directory [/usr/local/tomcat/webapps/examples] has finished
in [2,803] ms
30-Nov-2018 14:50:59.076 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
application directory [/usr/local/tomcat/webapps/ROOT]
30-Nov-2018 14:50:59.174 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
application directory [/usr/local/tomcat/webapps/ROOT] has finished in
[98] ms
30-Nov-2018 14:50:59.178 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
application directory [/usr/local/tomcat/webapps/host-manager]
30-Nov-2018 14:50:59.314 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
application directory [/usr/local/tomcat/webapps/host-manager] has
finished in [137] ms
30-Nov-2018 14:50:59.328 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
application directory [/usr/local/tomcat/webapps/manager]
30-Nov-2018 14:50:59.525 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
application directory [/usr/local/tomcat/webapps/manager] has finished
in [198] ms
30-Nov-2018 14:50:59.536 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
application directory [/usr/local/tomcat/webapps/docs]
30-Nov-2018 14:50:59.645 INFO [localhost-startStop-1]
org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
application directory [/usr/local/tomcat/webapps/docs] has finished in
[108] ms
30-Nov-2018 14:50:59.665 INFO [main]
org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler
["http-nio-8080"]
30-Nov-2018 14:50:59.781 INFO [main]
org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler
["ajp-nio-8009"]
30-Nov-2018 14:50:59.816 INFO [main]
org.apache.catalina.startup.Catalina.start Server startup in 61315 ms
Re: Fuseki as a Web application in Docker
Posted by Andy Seaborne <an...@apache.org>.
On 30/11/2018 14:13, Sorin Gheorghiu wrote:
> Hi,
>
> the first attempt to start fuseki as a web application within a Docker
> with Apache, Tomcat and Elasticsearch images succeded.
>
> But after a restart (i.e. docker-compose down/up) it failed with
> 'Illegal access' error. Moreover a reboot didn't help, the error still
> occurs.
>
> Do you have any idea wheater is this related to fuseki or not? As well
> any clue how to fix it?
It looks like it is from ElasticSearch.
just kill the tomcat or container - graceful shutdown is a nicety and
any systems has to survive a non-graceful shutdown.
Andy
>
> Thank you in advance
>
>
> 30-Nov-2018 14:49:58.857 INFO [main]
> org.apache.catalina.core.StandardEngine.startInternal Starting Servlet
> Engine: Apache Tomcat/8.5.35
> 30-Nov-2018 14:49:59.289 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployWAR Deploying web
> application archive [/usr/local/tomcat/webapps/fuseki.war]
> 30-Nov-2018 14:50:31.033 INFO [localhost-startStop-1]
> org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was
> scanned for TLDs yet contained no TLDs. Enable debug logging for this
> logger for a complete list of JARs that were scanned but no TLDs were
> found in them. Skipping unneeded JARs during scanning can improve
> startup time and JSP compilation time.
> 30-Nov-2018 14:50:55.757 SEVERE [localhost-startStop-1]
> org.apache.catalina.core.StandardContext.startInternal One or more
> listeners failed to start. Full details will be found in the appropriate
> container log file
> 30-Nov-2018 14:50:55.860 SEVERE [localhost-startStop-1]
> org.apache.catalina.core.StandardContext.startInternal Context [/fuseki]
> startup failed due to previous errors
> 30-Nov-2018 14:50:56.063 WARNING [localhost-startStop-1]
> org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads
> The web application [fuseki] appears to have started a thread named
> [elasticsearch[_client_][[timer]]] but has failed to stop it. This is
> very likely to create a memory leak. Stack trace of thread:
> java.lang.Thread.sleep(Native Method)
> org.elasticsearch.threadpool.ThreadPool$EstimatedTimeThread.run(ThreadPool.java:498)
> 30-Nov-2018 14:50:56.080 WARNING [localhost-startStop-1]
> org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads
> The web application [fuseki] appears to have started a thread named
> [elasticsearch[_client_][scheduler][T#1]] but has failed to stop it.
> This is very likely to create a memory leak. Stack trace of thread:
> sun.misc.Unsafe.park(Native Method)
> java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
> java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
> java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)
> java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
> java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074)
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> java.lang.Thread.run(Thread.java:748)
> 30-Nov-2018 14:50:56.104 WARNING [localhost-startStop-1]
> org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads
> The web application [fuseki] appears to have started a thread named
> [elasticsearch[_client_][transport_client_boss][T#1]] but has failed to
> stop it. This is very likely to create a memory leak. Stack trace of
> thread:
> sun.nio.ch.EPollArrayWrapper.epollWait(Native Method)
> sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269)
> sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:93)
> sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:86)
> sun.nio.ch.SelectorImpl.select(SelectorImpl.java:97)
> io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:746)
> io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:391)
> io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:858)
> java.lang.Thread.run(Thread.java:748)
> 30-Nov-2018 14:50:56.106 SEVERE [localhost-startStop-1]
> org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks
> The web application [fuseki] created a ThreadLocal with key of type
> [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@1ec7c10]) and a
> value of type [io.netty.util.internal.InternalThreadLocalMap] (value
> [io.netty.util.internal.InternalThreadLocalMap@45226f45]) but failed to
> remove it when the web application was stopped. Threads are going to be
> renewed over time to try and avoid a probable memory leak.
> 30-Nov-2018 14:50:56.120 SEVERE [localhost-startStop-1]
> org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks
> The web application [fuseki] created a ThreadLocal with key of type
> [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@1ec7c10]) and a
> value of type [io.netty.util.internal.InternalThreadLocalMap] (value
> [io.netty.util.internal.InternalThreadLocalMap@1593114a]) but failed to
> remove it when the web application was stopped. Threads are going to be
> renewed over time to try and avoid a probable memory leak.
> 30-Nov-2018 14:50:56.248 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployWAR Deployment of web
> application archive [/usr/local/tomcat/webapps/fuseki.war] has finished
> in [56,952] ms
> 30-Nov-2018 14:50:56.268 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
> application directory [/usr/local/tomcat/webapps/examples]
> 30-Nov-2018 14:50:58.528 INFO [elasticsearch[_client_][scheduler][T#1]]
> org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading
> Illegal access: this web application instance has been stopped already.
> Could not load
> [org.elasticsearch.common.util.concurrent.ThreadContext$ContextPreservingAbstractRunnable].
> The following stack trace is thrown for debugging purposes as well as to
> attempt to terminate the thread which caused the illegal access.
> java.lang.IllegalStateException: Illegal access: this web application
> instance has been stopped already. Could not load
> [org.elasticsearch.common.util.concurrent.ThreadContext$ContextPreservingAbstractRunnable].
> The following stack trace is thrown for debugging purposes as well as to
> attempt to terminate the thread which caused the illegal access.
> at
> org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading(WebappClassLoaderBase.java:1348)
>
> at
> org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1336)
>
> at
> org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1195)
>
> at
> org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1156)
>
> at
> org.elasticsearch.common.util.concurrent.ThreadContext.preserveContext(ThreadContext.java:273)
>
> at
> org.elasticsearch.common.util.concurrent.EsThreadPoolExecutor.wrapRunnable(EsThreadPoolExecutor.java:159)
>
> at
> org.elasticsearch.common.util.concurrent.EsThreadPoolExecutor.execute(EsThreadPoolExecutor.java:89)
>
> at
> org.elasticsearch.threadpool.ThreadPool$ThreadedRunnable.run(ThreadPool.java:455)
>
> at
> org.elasticsearch.threadpool.ThreadPool$LoggingRunnable.run(ThreadPool.java:419)
>
> at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at
> java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
>
> at
> java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
>
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>
> at java.lang.Thread.run(Thread.java:748)
>
> 30-Nov-2018 14:50:59.071 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
> application directory [/usr/local/tomcat/webapps/examples] has finished
> in [2,803] ms
> 30-Nov-2018 14:50:59.076 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
> application directory [/usr/local/tomcat/webapps/ROOT]
> 30-Nov-2018 14:50:59.174 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
> application directory [/usr/local/tomcat/webapps/ROOT] has finished in
> [98] ms
> 30-Nov-2018 14:50:59.178 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
> application directory [/usr/local/tomcat/webapps/host-manager]
> 30-Nov-2018 14:50:59.314 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
> application directory [/usr/local/tomcat/webapps/host-manager] has
> finished in [137] ms
> 30-Nov-2018 14:50:59.328 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
> application directory [/usr/local/tomcat/webapps/manager]
> 30-Nov-2018 14:50:59.525 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
> application directory [/usr/local/tomcat/webapps/manager] has finished
> in [198] ms
> 30-Nov-2018 14:50:59.536 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deploying web
> application directory [/usr/local/tomcat/webapps/docs]
> 30-Nov-2018 14:50:59.645 INFO [localhost-startStop-1]
> org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web
> application directory [/usr/local/tomcat/webapps/docs] has finished in
> [108] ms
> 30-Nov-2018 14:50:59.665 INFO [main]
> org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler
> ["http-nio-8080"]
> 30-Nov-2018 14:50:59.781 INFO [main]
> org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler
> ["ajp-nio-8009"]
> 30-Nov-2018 14:50:59.816 INFO [main]
> org.apache.catalina.startup.Catalina.start Server startup in 61315 ms
>
>