Leak Memory Error

[Claudia Roberta]

Hi guys!

Since yesterday, I'm having the following error when uploading Tomcat:

12-Sep-2023 21:29:44.140 GRAVE [main] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
12-Sep-2023 21:29:44.143 GRAVE [main] org.apache.catalina.core.StandardContext.startInternal Context [/sakai-onedrive-tool] startup failed due to previous errors
12-Sep-2023 21:29:44.154 ADVERTÊNCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [sakai-onedrive-tool] appears to have started a thread named [boot precache users] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java...@11.0.18/java.lang.Object.wait(Native Method)
 java...@11.0.18/java.lang.Object.wait(Object.java:328)
 java...@11.0.18/java.util.TimerThread.mainLoop(Timer.java:527)
 java...@11.0.18/java.util.TimerThread.run(Timer.java:506)
12-Sep-2023 21:29:44.169 ADVERTÊNCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [sakai-onedrive-tool] appears to have started a thread named [daily precache users] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java...@11.0.18/java.lang.Object.wait(Native Method)
 java...@11.0.18/java.lang.Object.wait(Object.java:328)
 java...@11.0.18/java.util.TimerThread.mainLoop(Timer.java:527)
 java...@11.0.18/java.util.TimerThread.run(Timer.java:506)
12-Sep-2023 21:29:44.170 ADVERTÊNCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [sakai-onedrive-tool] appears to have started a thread named [org.azeckoski.reflectutils.refmap.Finalizer] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java...@11.0.18/java.lang.Object.wait(Native Method)
 java...@11.0.18/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
 java...@11.0.18/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176)
 org.azeckoski.reflectutils.refmap.Finalizer.run(Finalizer.java:127)
12-Sep-2023 21:29:44.170 ADVERTÊNCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [sakai-onedrive-tool] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java...@11.0.18/java.lang.Object.wait(Native Method)
 java...@11.0.18/java.util.TimerThread.mainLoop(Timer.java:553)
 java...@11.0.18/java.util.TimerThread.run(Timer.java:506)
12-Sep-2023 21:29:44.171 ADVERTÊNCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [sakai-onedrive-tool] appears to have started a thread named [SakaiPresenceService.Maintenance] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java...@11.0.18/java.lang.Thread.sleep(Native Method)
 org.sakaiproject.presence.impl.BasePresenceService$Maintenance.run(BasePresenceService.java:794)
 java...@11.0.18/java.lang.Thread.run(Thread.java:829)
12-Sep-2023 21:29:44.171 ADVERTÊNCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [sakai-onedrive-tool] appears to have started a thread named [Sakai.SessionComponent.Maintenance] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java...@11.0.18/java.lang.Thread.sleep(Native Method)
 org.sakaiproject.tool.impl.SessionComponent$Maintenance.run(SessionComponent.java:600)
 java...@11.0.18/java.lang.Thread.run(Thread.java:829)
12-Sep-2023 21:29:44.172 ADVERTÊNCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [sakai-onedrive-tool] appears to have started a thread named [helpCP housekeeper] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java...@11.0.18/jdk.internal.misc.Unsafe.park(Native Method)
 java...@11.0.18/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
 java...@11.0.18/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2123)
 java...@11.0.18/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1182)
 java...@11.0.18/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:899)
 java...@11.0.18/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
 java...@11.0.18/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
 java...@11.0.18/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
 java...@11.0.18/java.lang.Thread.run(Thread.java:829)
12-Sep-2023 21:29:44.173 ADVERTÊNCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [sakai-onedrive-tool] appears to have started a thread named [helpCP connection adder] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 java...@11.0.18/jdk.internal.misc.Unsafe.park(Native Method)
 java...@11.0.18/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
 java...@11.0.18/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2123)
 java...@11.0.18/java.util.concurrent.LinkedBlockingQueue.poll(LinkedBlockingQueue.java:458)
 java...@11.0.18/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053)
 java...@11.0.18/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
 java...@11.0.18/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
 java...@11.0.18/java.lang.Thread.run(Thread.java:829)
12-Sep-2023 21:29:44.184 INFORMAÇÕES [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/opt/apache-tomcat-9.0.73/webapps/sakai-onedrive-tool.war] has finished in [56.355] ms

I'm using Sakai 22.2, Apache Tomcat/9.0.73, Linux 5.10.0-21-amd64 and java-11-openjdk-amd64. Can anyone help me?

Tks,

--

Claudia Moraes

Larc - Laboratório de Arquitetura e Redes de Computadores

[Markus Stetschnig]

Hi Claudia!

It looks like there might be more previous errors on startup that were causing this, could you share them if they are present?

--

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Markus Stetschnig
Software Developer at EDF

Website: https://www.edf.global
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[Hendrik Steller]

Hi,

those look like Tomcat's warnings about potential (classloader-)memory leaks
when redeploying a webapp (sakai-onedrive-tool.war).
If you have a webapp that starts background threads and don't include code to
stop those threads when the webapp gets undeployed, then afterwards there
might still be references around to the classes and objects from that
deployment which can't be garbage collected.

That means if you re-deploy that webapp a lot without restarting Tomcat, there
might be old, unused objects from previous deployments piling up.
To get rid of that garbage, you would have to restart Tomcat.

So if
a) Tomcat got it right ("_appears_ to have started, but failed to stop..")
and
b) you re-deploy that webapp _a_lot_(!) without restarting tomcat in between
and/or those uncollectable objects are really, really big

then you might eventually run out of memory after one of those re-deployments.

I don't know about you, but outside of hotfixes I rarely re-deploy single sakai
webapps in production without restarting tomcat, because if those updates
involve components/services or api packages outside of the webapp
(classloader), you will have to restart tomcat anyway for the changes to take
effect.

So I wouldn't worry too much about those messages unless you redeploy this
webapp _a_lot_ between tomcat restarts. And then a Tomcat restart would "fix"
this.
(Well, the actual fix would be for the webapp to do proper housekeeping, but as
said before, given Sakai's special structure with all the stuff deployed to
tomcat/lib and components, it shouldn't happen that often that one redeploys
webapps in production without restarting tomcat).


Regards,
Hendrik

[Claudia Roberta]

Hi guys!

I appreciate the responses.
In fact, I stop the Tomcat service, compile using Maven and start the Tomcat service again.
The Sakai platform has many tools. I tried disabling the OneDrive project, but the same error happened to another tool.
From what I researched about this error, I suspect it is something related to caching.
So, Hendrik's answer made sense to me. But, the problem is the number of tools. I wasn't even working on the OneDrive project when the error started. I was working on the Wiki.


As Marcus requested, the full error is attached.

If you can help me, I would appreciate it.

Regards,

Claudia

> I'm using Sakai 22.2, Apache Tomcat/9.0.73, Linux 5.10.0-21-amd64 and
> java-11-openjdk-amd64. Can anyone help me?
>
> Tks,

[Miguel Pellicer]

The stdout file will give you more information, it is not related to the one-drive project.

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-- 
-----------------------------------------------
Miguel Pellicer
CTO at EDF

Website: https://www.edf.global
LinkedIn: https://es.linkedin.com/company/entornosdeformacion
LinkedIn: https://www.linkedin.com/in/mpellicer-edf

Office Phone: +34 - 96 381 35 75

Request a meeting here: https://calendly.com/mpellicer

[Claudia Roberta]

Hi!

I appreciate your response!

We aren't interested in using the OneDrive tool, I disabled it. When I did this, the error was repeated:

14-Sep-2023 09:41:42.958 GRAVE [main] org.apache.catalina.core.StandardContext.startInternal One or more listeners failed to start. Full details will be found in the appropriate container log file
14-Sep-2023 09:41:42.962 GRAVE [main] org.apache.catalina.core.StandardContext.startInternal Context [/commons-tool] startup failed due to previous errors
14-Sep-2023 09:41:42.983 ADVERTÊNCIA [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [commons-tool] appears to have started a thread named [boot precache users] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

Any idea?

Regards,

Claudia

[Markus Stetschnig]

Do you have a catalina.out file at /opt/apache-tomcat-9.0.73/logs?

Markus

[Claudia Roberta]

Hi guys!

Markus,

Yes, I do.
I'm sending attached.

The work directory is cleaned, the previous months' logs are deleted and the MySQL server is restarted.
These procedures were recommended on a forum.

See the output with the tail command in attached.

Any idea?

Regards,

Claudia