upgrade new install on 22.04 version 2.22.2 with existing data fails. #510

phanohanover · 2023-03-16T15:57:53Z

phanohanover
Mar 16, 2023

Hi all,

I would like some help or guidance on standing up the latest version.
I tried various approaches but always getting the same error I don't understand.

Pulled 2.22.2 (kartoza)

Command:

docker run --mount type=bind,src=/etc/hosts,target=/etc/hosts,src=/geoserver/data_dir,target=/opt/geoserver/data_dir -e GEOSERVER_ADMIN_USER=kartoza  -e GEOSERVER_ADMIN_PASSWORD=myawesomegeoserver --restart always --log-opt max-size=2048m --name "maprisk_geoserver" -it -p 0.0.0.0:80:8080 -p 0.0.0.0:38080:8080 kartoza/geoserver:2.22.2

Starts with error (see blelow)

Jump into the container:

docker exec -it 644397da79b4 /bin/bash

So this folder HAS the right content it should...

root@644397da79b4:/opt/geoserver/data_dir

...
-rwxrwxrwx  1 geoserveruser geoserverusers  3631 Nov  1  2019 'Total Crime.sld'*
-rwxrwxrwx  1 geoserveruser geoserverusers  3631 Nov  1  2019  TotalCrime.sld*
-rwxrwxrwx  1 geoserveruser geoserverusers   313 Nov  1  2019  TotalCrime.xml*
-rwxrwxrwx  1 geoserveruser geoserverusers     0 Nov  1  2019  .updatepassword.lock*
drwxrwxrwx  2 geoserveruser geoserverusers     6 Nov  1  2019  uploads/
drwxrwxrwx  2 geoserveruser geoserverusers    29 May  9  2022  user_projections/
-rwxrwxrwx  1 geoserveruser geoserverusers   775 Nov  1  2019  wcs.xml*
-rwxrwxrwx  1 geoserveruser geoserverusers  1655 Nov  1  2019  wms.xml*
-rwxrwxrwx  1 geoserveruser geoserverusers   648 Nov  1  2019  wmts.xml*
drwxrwxrwx  5 geoserveruser geoserverusers    72 Nov  1  2019  workspaces/
-rwxrwxrwx  1 geoserveruser geoserverusers  2100 Mar 13 18:19  wps.xml*

Always getting same error:

16-Mar-2023 15:44:59.503 INFO [main] it.geosolutions.jaiext.JAIExt.registerOp Unable to register the descriptor related to the following operation: TIFF
16-Mar-2023 15:44:59.503 INFO [main] it.geosolutions.jaiext.JAIExt.registerOp Unable to register the descriptor related to the following operation: Threshold
16-Mar-2023 15:44:59.503 INFO [main] it.geosolutions.jaiext.JAIExt.registerOp Unable to register the descriptor related to the following operation: Transpose
16-Mar-2023 15:44:59.504 INFO [main] it.geosolutions.jaiext.JAIExt.registerOp Unable to register the descriptor related to the following operation: URL
16-Mar-2023 15:44:59.504 INFO [main] it.geosolutions.jaiext.JAIExt.registerOp Unable to register the descriptor related to the following operation: UnsharpMask
[Fatal Error] :-1:-1: Premature end of file.
16-Mar-2023 15:45:07.167 SEVERE [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
16-Mar-2023 15:45:07.168 SEVERE [main] org.apache.catalina.core.StandardContext.startInternal Context [/geoserver] startup failed due to previous errors
16-Mar-2023 15:45:07.951 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [geoserver] 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:
 [email protected]/java.lang.Object.wait(Native Method)
 [email protected]/java.util.TimerThread.mainLoop(Timer.java:553)
 [email protected]/java.util.TimerThread.run(Timer.java:506)
16-Mar-2023 15:45:07.952 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [geoserver] appears to have started a thread named [FileSystemWatcher-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
 [email protected]/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234)
 [email protected]/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2123)
 [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1182)
 [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:899)
 [email protected]/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1054)
 [email protected]/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114)
 [email protected]/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
 [email protected]/java.lang.Thread.run(Thread.java:829)
16-Mar-2023 15:45:07.952 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [geoserver] appears to have started a thread named [Timer-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 [email protected]/java.lang.Object.wait(Native Method)
 [email protected]/java.util.TimerThread.mainLoop(Timer.java:553)
 [email protected]/java.util.TimerThread.run(Timer.java:506)
16-Mar-2023 15:45:07.953 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [geoserver] appears to have started a thread named [EMF Reference Cleaner] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 [email protected]/java.lang.Object.wait(Native Method)
 [email protected]/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155)
 [email protected]/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176)
 org.eclipse.emf.common.util.CommonUtil$1ReferenceClearingQueuePollingThread.run(CommonUtil.java:70)
16-Mar-2023 15:45:07.953 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [geoserver] appears to have started a thread named [H2 File Lock Watchdog /opt/geoserver/data_dir/gwc/diskquota_page_store_h2/diskquota.lock.db] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
 [email protected]/java.lang.Thread.sleep(Native Method)
 org.h2.store.FileLock$1.run(FileLock.java:341)
 [email protected]/java.lang.Thread.run(Thread.java:829)
16-Mar-2023 15:45:07.954 SEVERE [main] org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks The web application [geoserver] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@3febe643]) and a value of type [org.springframework.security.core.context.SecurityContextImpl] (value [org.springframework.security.core.context.SecurityContextImpl@ffffffff: Null authentication]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
16-Mar-2023 15:45:07.954 SEVERE [main] org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks The web application [geoserver] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@60f7bd70]) and a value of type [org.geotools.referencing.wkt.Formatter] (value []) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
16-Mar-2023 15:45:07.955 SEVERE [main] org.apache.catalina.loader.WebappClassLoaderBase.checkThreadLocalMapForLeaks The web application [geoserver] created a ThreadLocal with key of type [java.lang.ThreadLocal.SuppliedThreadLocal] (value [java.lang.ThreadLocal$SuppliedThreadLocal@292e0532]) and a value of type [org.geowebcache.storage.CompositeBlobStore.StoreSuitabilityCheck] (value [EXISTING]) 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.
16-Mar-2023 15:45:07.962 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/geoserver] has finished in [24,859] ms
16-Mar-2023 15:45:07.962 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/ROOT]
16-Mar-2023 15:45:07.972 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/ROOT] has finished in [10] ms
16-Mar-2023 15:45:07.972 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/host-manager]
16-Mar-2023 15:45:07.985 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/host-manager] has finished in [13] ms
16-Mar-2023 15:45:07.985 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/docs]
16-Mar-2023 15:45:07.993 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/docs] has finished in [8] ms
16-Mar-2023 15:45:07.993 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/examples]
16-Mar-2023 15:45:08.095 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/examples] has finished in [102] ms
16-Mar-2023 15:45:08.099 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
16-Mar-2023 15:45:08.110 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [25483] milliseconds
16-Mar-2023 15:49:44.178 INFO [FileSystemWatcher-1] org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading Illegal access: this web application instance has been stopped already. Could not load [org.geoserver.platform.resource.FileSystemWatcher$Delta]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
	java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load [org.geoserver.platform.resource.FileSystemWatcher$Delta]. 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:1432)
		at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1420)
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1259)
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1220)
		at org.geoserver.platform.resource.FileSystemWatcher$Watch.pollDirectory(FileSystemWatcher.java:254)
		at org.geoserver.platform.resource.FileSystemWatcher$Watch.changed(FileSystemWatcher.java:211)
		at org.geoserver.platform.resource.FileSystemWatcher$1.run(FileSystemWatcher.java:342)
		at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
		at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305)
		at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305)
		at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
		at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
		at java.base/java.lang.Thread.run(Thread.java:829)
16-Mar-2023 15:50:09.192 INFO [FileSystemWatcher-1] org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading Illegal access: this web application instance has been stopped already. Could not load [org.geoserver.platform.resource.FileSystemWatcher$Delta]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
	java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load [org.geoserver.platform.resource.FileSystemWatcher$Delta]. 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:1432)
		at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1420)
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1259)
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1220)
		at org.geoserver.platform.resource.FileSystemWatcher$Watch.pollDirectory(FileSystemWatcher.java:249)
		at org.geoserver.platform.resource.FileSystemWatcher$Watch.changed(FileSystemWatcher.java:211)
		at org.geoserver.platform.resource.FileSystemWatcher$1.run(FileSystemWatcher.java:342)
		at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
		at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305)
		at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305)
		at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
		at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
		at java.base/java.lang.Thread.run(Thread.java:829)
16-Mar-2023 15:50:29.204 INFO [FileSystemWatcher-1] org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading Illegal access: this web application instance has been stopped already. Could not load [org.geoserver.platform.resource.FileSystemWatcher$Delta]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
	java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load [org.geoserver.platform.resource.FileSystemWatcher$Delta]. 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:1432)
		at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1420)
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1259)
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1220)
		at org.geoserver.platform.resource.FileSystemWatcher$Watch.pollDirectory(FileSystemWatcher.java:254)
		at org.geoserver.platform.resource.FileSystemWatcher$Watch.changed(FileSystemWatcher.java:211)
		at org.geoserver.platform.resource.FileSystemWatcher$1.run(FileSystemWatcher.java:342)
		at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
		at java.base/java.util.concurrent.FutureTask.runAndReset(FutureTask.java:305)
		at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:305)
		at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
		at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
		at java.base/java.lang.Thread.run(Thread.java:829)

NyakudyaA · 2023-03-16T16:14:47Z

NyakudyaA
Mar 16, 2023
Maintainer

It sounds like they are some issues with the geoserver data dir. Please check what permissions are for the geoserver_data dir.
try running:

chown -R $user:$user geoserver_data_dir

or alternatively, mount the user to inherit local folder perms in the container with https://github.com/kartoza/docker-geoserver/blob/develop/scripts/entrypoint.sh#L8

3 replies

phanohanover Mar 16, 2023
Author

My host user is ubuntu.
(777 on the whole /geoserver/data_dir folder on the host)

Should I have a geoserveruser on the host? since I think this is what gets mounted on the container?

phanohanover Mar 16, 2023
Author

Or should I specify the user at run command ?

NyakudyaA Mar 16, 2023
Maintainer

You can specify a user at run time, and pass the same uid of the files

phanohanover · 2023-03-16T18:59:10Z

phanohanover
Mar 16, 2023
Author

docker run --mount type=bind,src=/etc/hosts,target=/etc/hosts,src=/geoserver/data_dir,target=/opt/geoserver/data_dir -e USER=ubuntu -e GROUP_NAME=ubuntu -e GEOSERVER_UID=1000 -e GEOSERVER_GID=1000 -e GEOSERVER_ADMIN_USER=kartoza -e GEOSERVER_ADMIN_PASSWORD=myawesomegeoserver --restart always --log-opt max-size=2048m --name "phano_geoserver" -it -p 0.0.0.0:80:8080 -p 0.0.0.0:38080:8080 phano/geoserver:2.22.2

My local mount on the host /geoserver* belongs to ubuntu.ubuntu (uid & gid 1000) ...

Getting the same error
Any other suggestion?

1 reply

phanohanover Mar 17, 2023
Author

I tried both and still face the same issue.
I can access the volume when connected to the container. ownership appears as I set it too from Dockerfile.
Would there be a specific file that needs specific owner?

NyakudyaA · 2023-07-06T20:05:55Z

NyakudyaA
Jul 6, 2023
Maintainer

Please try with the latest image and if issue doesn't exists please close

0 replies

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upgrade new install on 22.04 version 2.22.2 with existing data fails. #510

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